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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/vmatch">Debian Med / vmatch</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/4ae5e4c0ab36b0c1a87e60babdc84951adb86a32">4ae5e4c0</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-02T01:02:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more extended description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/5e7ad947915e16517bc3b7780a8eace480df612d">5e7ad947</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-02T01:02:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">install .pr files in dev pkg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/1f933a2e2d48905ab096f72979e9e01e746809ae">1f933a2e</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-02T01:03:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add man pages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/0e22fabbdc4b534b37cbb9f41705ad696eddebce">0e22fabb</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-02T01:03:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">include scripts outside /usr/bin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/d54735101a5a0a8a2fced27bef58e60540a1ed7b">d5473510</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-02T01:05:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">include source for selector functions
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a9e40ad687099998cf394937c45b1965a479e01e">
debian/libvmatch-dev.install
</a>
</li>
<li class="file-stats">
<a href="#939c88e44acf5f7c961c29e29ac2d76cd4592a65">
<span class="new-file">
+
debian/mansrc/chain2dim.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#0a2df280068582b82bd89c6b195dba49da224cc5">
<span class="new-file">
+
debian/mansrc/matchcluster.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#9efea92dfb9db2773e7daa76663f3cc4aac38616">
<span class="new-file">
+
debian/mansrc/mkdna6idx.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#2fe9f83a3fbbd0a33629765ce056d045b3bddb86">
<span class="new-file">
+
debian/mansrc/mkvtree.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#8f79a1cf7d9016bb319fb9accf12f2a7366fb9e7">
<span class="new-file">
+
debian/mansrc/vendian.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#c9840feea7bd248a5e5945c1d6bd1101fadd1800">
<span class="new-file">
+
debian/mansrc/vmatch.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44">
<span class="new-file">
+
debian/mansrc/vmatchselect.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#922206448ae2603875a84662964d4357e349c10f">
<span class="new-file">
+
debian/mansrc/vseqinfo.1.adoc
</span>
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</li>
<li class="file-stats">
<a href="#1341db262da2e1b8c55a754dfa788196d5cd8221">
<span class="new-file">
+
debian/mansrc/vseqselect.1.adoc
</span>
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</li>
<li class="file-stats">
<a href="#e5ff47c5818269ff70ab3f6450d5ed23fcc8f77d">
<span class="new-file">
+
debian/mansrc/vstree2tex.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#b121163685f8876827038491dff878668885db28">
<span class="new-file">
+
debian/mansrc/vsubseqselect.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#924314810df1cb51391abf924d0a92ec6f02374c">
debian/vmatch.install
</a>
</li>
<li class="file-stats">
<a href="#57fac72d97fcc44b28a8e50d0ad4154c33ee48de">
<span class="new-file">
+
debian/vmatch.manpages
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,4 +32,5 @@ Depends: ${shlibs:Depends},</td>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> ${misc:Depends}</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Description: development headers and static library for Vmatch</span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> This package contains C development headers and a static library to</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> build custom programs utilizing Vmatch.</span></pre>
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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> build custom programs and selector functions utilizing Vmatch.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> It also includes example source code for selector functions.</span></pre>
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<br>
</li>
<li id="a9e40ad687099998cf394937c45b1965a479e01e">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#a9e40ad687099998cf394937c45b1965a479e01e"><strong>debian/libvmatch-dev.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">libfiles</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">a</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">h</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">pr</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Vmatch</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">pr</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">SELECT</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span></span></pre>
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<li id="939c88e44acf5f7c961c29e29ac2d76cd4592a65">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#939c88e44acf5f7c961c29e29ac2d76cd4592a65"><strong>debian/mansrc/chain2dim.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># chain2dim(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">chain2dim - two-dimensional match chaining</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*chain2dim* [options] <matchfile></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*-global* <param>:: </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Global chaining. Optional parameter "gc" switches on gap costs (according to</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> L1-model). Optional parameter "ov" means that overlaps between matches are</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> allowed.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">*-local* <param>::</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Compute local chains (according to L1-model).</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> If no parameter is given, compute local chains with maximum score.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> If parameter is given, this must be a positive number optionally followed by</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> the character b or p. If only the number, say k, is given, this is the</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> minimum score of the chains output.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> If a number is followed by character b, then output all chains with the</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> largest k scores. If a number is followed by character p, then output all</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> chains with scores at most k percent away from the best score.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">*-wf* <factor>::</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> Specify weight factor > 0.0 to obtain the score of a fragment. Requires one</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> of the options *-local*, *-global gc* or *-global ov*.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">*-maxgap* <width>::</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Maximal width of gap in chain.</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">*-outprefix* <prefix>::</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> Specify prefix of files to output chains.</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">*-withinborders*::</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> Only compute chains which do not cross sequence borders (not possible for</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> matches in open format).</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">*-thread* <keywords...>::</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> Thread the chains, i.e. close the gaps. Accepts an optional list of keywords</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> "minlen1 minlen2 maxerror1 maxerror2", each followed by a number specifies</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> the minimum length and the maximum error rate of thread.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> 1 refers to match instance in indexed sequence, 2 refers to matching</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> instance in query.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">*-silent*::</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> Do not output the chains and only report their lengths and scores.</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">*-v*::</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> Be verbose.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> Show help.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">## SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">vmatch(1)</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#0a2df280068582b82bd89c6b195dba49da224cc5"><strong>debian/mansrc/matchcluster.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># matchcluster (1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">matchcluster - match clustering</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*matchcluster* [options] <matchfile></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*-erate* <value>::</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Specify maximum error rate in range [0,100] for similarity clustering.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">*-gapsize* <size>::</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Specify maximum gap size for gap clustering.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">*-overlap* <percentage>::</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Specify minimum percentage of overlap for overlap clustering.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">*-outprefix* <string>::</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Specify prefix of files to output clusters.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> Show help.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">## SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">vmatch(1)</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#9efea92dfb9db2773e7daa76663f3cc4aac38616"><strong>debian/mansrc/mkdna6idx.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># mkdna6idx(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">mkdna6idx - generate a six frame translation index</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*mkdna6idx* [options] <indexname></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*mkdna6idx* is very similar to *mkvtree*. While *mkvtree* can handle sequences</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">over arbitrary alphabets, *mkdna6idx* requires DNA-sequences as input. It</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">generates two indices, namely:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* A flat index "indexname" for the the given DNA sequences. It mainly consists</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> of the two files "indexname.tis" and "indexname.ois". This index is mainly</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> used for output purpose.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">* An index "indexname.6fr" for the given DNA sequences translated in all six</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> reading frames.This is used for computing the matches.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Please also see the Vmatch manual for a more detailed explanation of the usage.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">*-db* <file>::</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Specify database files (mandatory).</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">*-smap* <file>::</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Specify file containing a symbol mapping. This describes the grouping of</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> symbols. It is possible to set the environment variable MKVTREESMAPDIR</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> to the path where these files can be found.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">*-transnum* <table>::</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> Perform six frame translation. Specify codon translation table by a number</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1):</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> 1 Standard</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> 2 Vertebrate Mitochondrial</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> 3 Yeast Mitochondrial</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> 5 Invertebrate Mitochondrial</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> 9 Echinoderm Mitochondrial</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> 10 Euplotid Nuclear</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> 11 Bacterial</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> 12 Alternative Yeast Nuclear</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> 13 Ascidian Mitochondrial</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> 14 Flatworm Mitochondrial</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> 15 Blepharisma Macronuclear</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> 16 Chlorophycean Mitochondrial</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> 21 Trematode Mitochondrial</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> 22 Scenedesmus Obliquus Mitochondrial</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> 23 Thraustochytrium Mitochondrial</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">*-indexname* <string>::</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> Specify name for index to be generated.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">*-cpl*::</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> Use reverse complement of the input sequence.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">*-tis*::</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> Output transformed input sequences (tistab) to file.</span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">*-ois*::</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> Output original input sequences (oistab) to file.</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">*-maxdepth* <len>::</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> Restrict the sorting to prefixes of the given length.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">*-v*::</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> Verbose mode.</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">*-version*::</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> Show the version of the Vmatch package</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">*-help*::</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> Show help.</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">## SEE ALSO</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">mkvtree(1)</span></pre>
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<li id="2fe9f83a3fbbd0a33629765ce056d045b3bddb86">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#2fe9f83a3fbbd0a33629765ce056d045b3bddb86"><strong>debian/mansrc/mkvtree.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># mkvtree(1)</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">mkvtree - construct index for sequence</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*mkvtree* [options]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">The program *mkvtree* constructs an index for a given set of sequences. These</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">are given as a list of input files. The sequences are referred to as database</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">sequences. They can be over any given alphabet. The alphabet can be the DNA</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">alphabet, or the protein alphabet, or any other alphabet consisting of</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">printable characters. An alphabet is specified by a file storing a symbol</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">mapping. The index consists of several files, the index files. Each such file</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">stores a different table. The user specifies which tables (i.e. which part of</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">the index) is written to a file, using one of eight output options, or a</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">single option specifying that all tables are written to file. </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">We support the following formats for the input files. They are recognized</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">according to the first non-whitespace symbol in the file.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">* multiple FASTA format: If the file begins with the symbol ">", then this</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> file is considered to be a file in multiple FASTA format (i.e. it contains</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> one or more sequences). Each line starting with the symbol ">" contains</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> the description of the sequence following it. Each line not</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> starting with the symbol ">" contains the sequence. Empty lines are allowed</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> and ignored when reading the input.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">* multiple EMBL/SWISSPROT format: If the file begins with the string "ID",</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> then this file is considered to be a file in multiple EMBL format (i.e.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> containing one or more sequences, each in EMBL format). The information</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> contained in the "ID" and "DE" lines is taken as the description of the</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> corresponding sequence. The EMBL format is identical to the SWISSPROT</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> format (w.r.t. the information we need to extract from such entries).</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> So one can also use files in multiple SWISSPROT format as input.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">* multiple GENBANK format: If the file begins with the string "LOCUS", then</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> this file is considered to be a file in multiple GENBANK format (i.e.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> containing one or more entries in GENBANK format). The information</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> contained in the "LOCUS" and the "DEFINITION" lines is taken as the</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> description of the corresponding sequence.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">* plain format: If the file does not begin with the symbol ">" or the strings</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> "ID" or "LOCUS", then the file is taken verbatim. That is, the entire file</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> is considered to be the input sequence (whitespaces are not ignored).</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">There is no special option necessary to tell the program the sequence format.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">It automatically detects the appropriate format, according to the rules given</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">above. If none of the above rules apply, then the program cannot recognize the</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">input format and exits with error code 1. In such a case please check you</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">input files for if they are conform with the input formats above. Another good</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">solution is to use a more versatile sequence format transformation programs</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">(e.g. *readseq*) to first generate multiple FASTA files and then feed this</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">into *mkvtree*.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Today many files containing sequence files are provided compressed by the</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">program *gzip*. To simplify the use of these files, *mkvtree* also accepts</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">gzipped input files. These files must have the ending ".gz". The gzipped</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">formatted files are gunzipped internally and then processed as any other</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">file.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">## OPTIONS</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">*-db* <file>::</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> Specify database files (mandatory).</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">*-smap* <file>::</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> Specify file containing a symbol mapping. This describes the grouping of</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> symbols. It is possible to set the environment variable MKVTREESMAPDIR</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> to the path where these files can be found.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">*-dna*::</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> Input is DNA sequence.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">*-protein*::</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> Input is Protein sequence.</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">*-indexname* <string>::</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> Specify name for index to be generated.</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">*-pl* <length>::</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> Specify prefix length for bucket sort.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
</td>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> Recommendation: use without argument; then a reasonable prefix length is automatically determined.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
</td>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">*-tis*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
</td>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> Output transformed input sequences (tistab) to file.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
</td>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
</td>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">*-ois*::</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> Output original input sequences (oistab) to file.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
</td>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
</td>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">*-suf*::</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> Output suffix array (suftab) to file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
</td>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
</td>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">*-sti1*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> Output reduced inverse suffix array (sti1tab) to file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
</td>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">*-bwt*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> Output Burrows-Wheeler Transformation (bwttab) to file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">*-bck*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> Output bucket boundaries (bcktab) to file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">*-skp*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> Output skip values (skptab) to file.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">*-lcp*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> Output longest common prefix lengths (lcptab) to file.</span>
</pre>
</td>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">*-allout*::</span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> Output all index tables to files.</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
</pre>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">*-maxdepth* <len>::</span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> Restrict the sorting to prefixes of the given length.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">*-v*::</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> Verbose mode</span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">*-version*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">*-help*::</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> Show help.</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">## RETURNS</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">If an error occurs, the program exits with error code 1. Otherwise, the exit code is 0. </span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
</pre>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">## SEE ALSO</span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">mkdna6idx(1)</span></pre>
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<li id="8f79a1cf7d9016bb319fb9accf12f2a7366fb9e7">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#8f79a1cf7d9016bb319fb9accf12f2a7366fb9e7"><strong>debian/mansrc/vendian.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vendian(1)</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vendian - helper tool for endianness conversion</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vendian* bytes filename</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">This is used by the *vmigrate.sh* script to perform index conversion.</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#c9840feea7bd248a5e5945c1d6bd1101fadd1800"><strong>debian/mansrc/vmatch.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vmatch(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vmatch - solve matching tasks</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vmatch* [options] indexname</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The program *vmatch* allows one to solve a multitude of different matching</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">tasks over an index constructed by *mkvtree*. Each matching task is solved by</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">a combination of options specifying</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* the input,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">* the kind of matches sought,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">* additional constraints on the matches,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">* the direction of the matches (in case of DNA),</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">* the kind of postprocessing to be done,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">* the output mode and output format.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Additionally, if there is more than one algorithm to solve a certain matching</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">task, *vmatch* allows to specify which algorithm is to be used. </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">*vmatch* allows to compute the following kinds of matches:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">. match all substrings of the database sequences against itself. The matches</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> can be one of the following kinds:</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.. branching tandem repeats, i.e. repeats where the two instances of the</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> repeat occur at consecutive positions</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.. maximal repeats, i.e. pairs of maximal substrings occurring more than</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> once in the database sequences</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.. supermaximal repeats, i.e. pairs of maximal substrings occurring more than</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> once in the database sequences, but not in any other maximal repeat</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">. match a set of query sequences (given in an extra query file) against the</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> index. The matches can be one of the following kinds:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.. maximal substring matches, i.e. the substrings of the query sequences</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> matching substrings of the database sequences. All matches exceeding some</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> minimum length,extended maximally to the left and to the right, are reported.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.. maximal unique matches, i.e. the substrings of the query sequences matching</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> substrings of the database sequences. A match is reported if it is unique in</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> the database sequences as well as in the query sequences.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.. complete matches, i.e. a query sequence must completely match (i.e. from the</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> first character to the last character) a substring of the database sequences.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">For all these match kinds, the matches themselves can be direct or palindromic</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">(i.e. on the reverse strand, in case of DNA sequences). If required, DNA</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">sequences are translated into six reading frames and the matches are computed</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">on the protein level, and reported on the DNA level. Besides exact matches,</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">also degenerate matches with a maximal number of errors (insertions, deletions,</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">and mismatches) are supported. Moreover, degenerate matches can be derived</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">from exact matches by extending these using a greedy extension strategy. This</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">does not apply to complete matches. For all different match kinds, the matches</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">delivered by *vmatch* can be selected according to their E-value, their</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">identity value, or their match score.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">In the default case, a match is reported as a formatted row of numbers,</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">containing its lengths, the positions where it occurs, the E-value, the number</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">of errors it contains, the match score, and the identity value. Optionally, an</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">alignment of the sequences that are involved in the match can be reported.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">An important feature of *vmatch* is the capability of directly postprocessing</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">the matches found in the following ways:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">. inverse output, i.e. report substrings of the database sequences or the query</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> sequences not covered by a match</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">. masking substrings of the database sequences or the query sequences covered</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> by a match</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">. clustering of a set of database sequences according to the matches found</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> between these sequences. The output of this option can be a representation of</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> the clusters, or a set of sequences each being representative for a cluster.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">. chaining of a set of matches, i.e. finding optimal subsets of all matches</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> which do not cross</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">. clustering of matches according to the pairwise similarities on the sequences</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> involved inthe match</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">. clustering of matches according to the positions where they occur</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Finally, to accommodate many more kinds of user defined post processing tasks,</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">*vmatch* provides the concept of selection functions. These provide an open</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">interface which allow arbitrary on-the-fly postprocessing of the matches</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">without output and parsing of the matches. For more details on this concept,</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">see the manual. </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">*-q* <file>::</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> Specify files containing queries to be matched.</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">*-dnavsprot* <table>::</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> Perform six frame translation. Specify codon translation table by a number</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> in the range [1,23] except for 7, 8, 17, 18, 19 and 20; (default is 1):</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> 1 Standard</span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> 2 Vertebrate Mitochondrial</span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> 3 Yeast Mitochondrial</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> 4 Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma</span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> 5 Invertebrate Mitochondrial</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> 6 Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> 9 Echinoderm Mitochondrial</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> 10 Euplotid Nuclear</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> 11 Bacterial</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> 12 Alternative Yeast Nuclear</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> 13 Ascidian Mitochondrial</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> 14 Flatworm Mitochondrial</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> 15 Blepharisma Macronuclear</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> 16 Chlorophycean Mitochondrial</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> 21 Trematode Mitochondrial</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> 22 Scenedesmus Obliquus Mitochondrial</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> 23 Thraustochytrium Mitochondrial</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">*-tandem*::</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> Compute right branching tandem repeats.</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">*-supermax*::</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> Compute supermaximal matches.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">*-mum*::</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> Compute maximal unique matches.</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">*-complete*::</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> Specify that query sequences must match completely.</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">*-dbnomatch* <arg>::</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> Mask all database substrings containing a match; optional argument:</span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> * keepleft means to not mask the left instance</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> of a match</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> * keepright means to not mask the right instance</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> of a match</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> * keepleftifsamesequence means to not mask the left instance</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> of the match if the right instance occurs</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> in the same sequence</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> * keeprightifsamesequence means to not mask the right instance</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> of the match if the left instance occurs</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> in the same sequence</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">*-qnomatch*::</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> Show all query substrings not containing a match.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">*-dbmaskmatch* <arg>::</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> Mask all database substrings containing a match; optional argument:</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> * keepleft means to not mask the left instance</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> of a match</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> * keepright means to not mask the right instance</span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> of a match</span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> * keepleftifsamesequence means to not mask the left instance</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> of the match if the right instance occurs</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> in the same sequence</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> * keeprightifsamesequence means to not mask the right instance</span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> of the match if the left instance occurs</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> in the same sequence</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> </span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">*-qmaskmatch*::</span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> Mask all query substrings containing a match.</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">*-pp*::</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> Generic postprocessing of matches.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">*-online*::</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> Run algorithms online without using the index.</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">*-qspeedup* <level>::</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> Specify speedup level when matching queries (0: fast, 2: faster; default is 2),</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> beware of time/space tradeoff.</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">*-d*::</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> Compute direct matches (default).</span>
</pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"></span>
</pre>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">*-p*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> Compute palindromic (i.e. reverse complemented matches).</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"></span>
</pre>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">*-h* <dist>::</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> Specify the allowed hamming distance > 0. In combination with option</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> *-complete* one can switch on the percentage search mode or the best</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> search mode for the percentage search mode use an argument of the</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> form ip (where i is a positive integer). This means that up to</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> i*100/m mismatches are allowed in a match of a query of length m.</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> For the best search mode use an argument of the form ib where i is a</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> positive integer. This means that in a first phase the minimum threshold q</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> is determined such that there is still a match with q mismatches. q is in</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> the range 0 to i*100/m.</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">*-e* <dist>::</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> Specify the allowed edit distance > 0. In combination with option</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> *-complete* one can switch on the percentage search mode or the best</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> search mode for the percentage search mode use an argument of the</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> form ip (where i is a positive integer). This means that up to </span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> i*100/m differences are allowed in a match of a query of length m.</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> For the best search mode use an argument of the form ib where i is a</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> positive integer. This means that in a first phase the minimum threshold q</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> is determined such that there is still a match with q differences. q is in</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> the range 0 to i*100/m.</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">*-allmax*::</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> Show all maximal matches in the order of their computation.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">*-seedlength* <length>::</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> Specify the seed length.</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">*-hxdrop* <value>::</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> Specify the xdrop value for hamming distance extension.</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">*-exdrop* <value>::</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> Specify the xdrop value for edit distance extension.</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">*-i*::</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> Give information about number of different matches.</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">*-dbcluster* <args>::</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> Cluster the database sequences.</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> * first argument is percentage of shorter string</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> to be included in match,</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> * second argument is percentage of larger string</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> to be included in match,</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> * third optional argument is filenameprefix,</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> * fourth optional argument is (minclustersize, maxclustersize)</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">*-nonredundant*::</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> Generate file with non-redundant set of sequences; only works together</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> with option *-dbcluster*.</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">*-selfun* <file>::</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> Specify shared object file containing selection function.</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">*-l* <length>::</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> Specify that match must have the given length, optionally specify minimum</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> and maximum size of gaps between repeat instances.</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">*-leastscore* <score>::</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> Specify the minimum score of a match.</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">*-evalue* <value>::</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> Specify the maximum E-value of a match.</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">*-identity* <value>::</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> Specify minimum identity of match in range [1..100%].</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">*-sort* <mode>::</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> Sort the matches, additional argument is mode:</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> la: ascending order of length</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> ld: descending order of length</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> ia: ascending order of first position</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> id: descending order of first position</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> ja: ascending order of second position</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> jd: descending order of second position</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> ea: ascending order of Evalue</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> ed: descending order of Evalue</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> sa: ascending order of score</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> sd: descending order of score</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> ida: ascending order of identity</span>
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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> idd: descending order of identity</span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">*-best* <n>::</span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> Show the best matches (those with smallest E-values), default is best 50.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">*-s*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> Show the alignment of matching sequences.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">*-showdesc*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
</td>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> Show sequence description of match.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">*-f*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> Show filename where match occurs.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"></span>
</pre>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">*-absolute*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
</td>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> Show absolute positions.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">*-nodist*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
</td>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> Do not show distance of match.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
</td>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">*-noevalue*::</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
</td>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> Do not show E-value of match.</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
</td>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">*-noscore*:: </span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> Do not show score of match.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"></span>
</pre>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">*-noidentity*::</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> Do not show identity of match.</span>
</pre>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">*-v*::</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> Verbose mode.</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">*-version*::</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
</pre>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">*-help*::</span>
</pre>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> Show basic options.</span>
</pre>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">*-help+*::</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> Show all options.</span>
</pre>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"></span>
</pre>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">## SEE ALSO</span>
</pre>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">vmatchselect(1)</span></pre>
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<li id="03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44"><strong>debian/mansrc/vmatchselect.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vmatchselect(1)</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vmatchselect - sort and select matches</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vmatchselect* [options] matchfile</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*vmatchselect* allows one to select interesting matches from the output of</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">vmatch as specified by user-defined criteria. It delivers matches of chosen</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">length, degeneracy or significance into further analysis routines.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">*vmatchselect* removes from the input all those matches that are contained in</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">another match. To do this efficiently, the matches are sorted by their</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">position in the database sequence, and hence in the order in which the matches</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">are output, unless the user specifies otherwise. Moreover, the sequences of</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">the virtual suffix tree for which the match filewas produced can be clustered</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">according to the matches. The input for *vmatchselect* is a file produced by</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">vmatch, called a match file.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">The output of *vmatchselect* goes to standard output and is sorted in</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">ascending order of the positions of the left instance of a match. Two matches</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">where the left instance occurs at the same position, are sorted in descending</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">order of their length. Two matches of the same length where the left instance</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">occurs in the same position, are sorted in ascending order of the position of</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">the right instance of the match.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">*vmatchselect* provides a subset of the options of *vmatch*.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">The main difference to *vmatch* is that *vmatchselect* gets the matches from</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">a match file, while *vmatch* computes the matches from scratch. Therefore</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">options specifying the index and/or the query sequences to be matched, as well</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">as options specifying how to match are not available in *vmatchselect*.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">The options of *vmatchselect* have the same meaning as in the program *vmatch*.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Thus, for a description, see the corresponding documentation. Note that</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">*vmatchselect* also allows to use the option "-dbcluster". If *vmatchselect*</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">is called with this option, then it parses the given match file and performs</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">single linkage clustering based on the matches in this file.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Thus *vmatch* and *vmatchselect* allow to perform hierarchical clustering.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">In a first step an initial set of matches with loose matching criteria is</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">computed, using *vmatch*. Then one clusters these matches by calling</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">*vmatchselect*. In a second round one applies more strict choices for the</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">matches by the using the options "-l", "-leastscore", "-evalue", or</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">"-identity", etc. This allows stepwise refinement of clusters without much</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">computational effort and no new index construction for the sequence of a</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">cluster. The output of *vmatchselect* is the same as the output of *vmatch*.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">*-dbcluster* <args>::</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> Cluster the database sequences.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> * first argument is percentage of shorter string</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> to be included in match,</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> * second argument is percentage of larger string</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> to be included in match,</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> * third optional argument is filenameprefix,</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> * fourth optional argument is (minclustersize, maxclustersize)</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">*-nonredundant*::</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> Generate file with non-redundant set of sequences; only works together</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> with option *-dbcluster*.</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">*-selfun* <file>::</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> Specify shared object file containing selection function.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">*-l* <length>::</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> Specify that match must have the given length, optionally specify minimum</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> and maximum size of gaps between repeat instances.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">*-leastscore* <score>::</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> Specify the minimum score of a match.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">*-evalue* <value>::</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> Specify the maximum E-value of a match.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">*-identity* <value>::</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> Specify minimum identity of match in range [1..100%].</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">*-sort* <mode>::</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> Sort the matches, additional argument is mode:</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> la: ascending order of length</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> ld: descending order of length</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> ia: ascending order of first position</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> id: descending order of first position</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> ja: ascending order of second position</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> jd: descending order of second position</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> ea: ascending order of Evalue</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> ed: descending order of Evalue</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> sa: ascending order of score</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> sd: descending order of score</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> ida: ascending order of identity</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> idd: descending order of identity</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">*-best* <n>::</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> Show the best matches (those with smallest E-values), default is best 50.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">*-s*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> Show the alignment of matching sequences.</span>
</pre>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"></span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">*-showdesc*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> Show sequence description of match.</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></span>
</pre>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">*-f*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
</td>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> Show filename where match occurs.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">*-absolute*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> Show absolute positions.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">*-nodist*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> Do not show distance of match.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">*-noevalue*::</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> Do not show E-value of match.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">*-noscore*:: </span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> Do not show score of match.</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">*-noidentity*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> Do not show identity of match.</span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">*-v*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> Verbose mode.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">*-version*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">*-help*::</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> Show help.</span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"></span>
</pre>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">## SEE ALSO</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>
</pre>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">vmatch(1)</span></pre>
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<li id="922206448ae2603875a84662964d4357e349c10f">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#922206448ae2603875a84662964d4357e349c10f"><strong>debian/mansrc/vseqinfo.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vseqinfo(1)</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vseqinfo - obtain sequence information from index</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vseqinfo* indexname</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">*vseqinfo* echoes for each database sequence its length and its description.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The program has no options. It takes exactly one argument, namely the index</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">name. The output goes to standard output.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">## SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">vseqselect(1)</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#1341db262da2e1b8c55a754dfa788196d5cd8221"><strong>debian/mansrc/vseqselect.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vseqselect(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vseqselect - print selected sequences from index</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vseqselect* [options] indexname</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">The program *vseqselect* selects sequences from a given index and prints them</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">on standard output.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">*-minlength*::</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Specify the minimal length of the sequences to be selected.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">*-maxlength* <length>::</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Specify the maximal length of the sequences to be selected.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">*-randomnum* <n>::</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Specify the number of random sequences to be selected.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">*-randomlength* <length>::</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Specify the minimal total length of the random sequences to be selected.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">*-seqnum* <filename>::</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Select the sequences with numbers given in filename.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Show the version of the Vmatch package</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> Show help.</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vstree2tex(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vstree2tex - pretty-print a virtual tree</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vstree2tex* [options] indexname</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">The program *vstree2tex* produces a representation of a virtual suffix tree</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">in LATEX format and print it to standard output. Note that *vstree2tex*</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">should only be used for very small indexes since it produces large output</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">files.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Suppose the total length of all sequences in the index is n. If the option</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">*-s* is not used, then the output size of *vstree2tex* is about 10n bytes</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">per option (plus some constant number of bytes for the header and the footer</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">of the LATEX file). If the option *-s* is used, then the size of the output</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">is proportional to n^2. </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">The program is mainly designed for debugging a program based on the index and</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">for educational purposes.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">## OPTIONS</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">*-s*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> Output suffixes.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">*-tis*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Output tistab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">*-ois*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> Output oistab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">*-suf*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> Output suftab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">*-sti1*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> Output small inverse suftab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">*-bwt*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Output bwttab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">*-bck*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> Output bcktab in vertical mode.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">*-bckhz*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> Output bcktab in horizontal mode.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">*-lcp*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> Output lcptab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">*-skp*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> Output skptab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">*-cfr*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> Output cfrtab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">*-crf*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> Output crftab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">*-lsf*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> Output lsftab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">*-sti*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> Output inverse suftab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">*-cld*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> Output cldtab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">*-iso*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> Output isotab.</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> Show the version of the Vmatch package.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> Show help.</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#b121163685f8876827038491dff878668885db28"><strong>debian/mansrc/vsubseqselect.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># vsubseqselect(1)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">vsubseqselect - print selected subsequences from index</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*vsubseqselect* [options] indexname</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">The program *vseqselect* selects subsequences from a given index and prints</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">them on standard output, either line by line or in FASTA format. The selection</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">can either be random or according to position ranges specified by the user.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Please refer to the manual for more detailed explanations.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">*-minlength*::</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Specify the minimal length of the substrings to be selected.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">*-maxlength* <length>::</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Specify the maximal length of the substrings to be selected.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">*-snum* <n>::</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Specify the number of random substrings to be selected.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">*-range* <pos> <pos>::</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Specify the first and last position of the substring to be selected.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">*-seq* <length> <number> <pos>:: </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Specify length, number, and relative position of the substring to be selected.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> Show the version of the Vmatch package</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> Show help.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"># </span>DH_VERBOSE := 1</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">DH_VERBOSE := 1</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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6
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PATH:=$(PATH):$(CURDIR)/src/bin</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,9 @@ export WORKVSTREESRC=$(CURDIR)/src</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">override_dh_auto_clean:</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> rm -rf debian/man</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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12
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_auto_build:</span>
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13
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> cd src && mklink.sh linux-gcc-64</span>
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14
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> cd src && make licensemanager=no $*</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +21,7 @@ override_dh_auto_install:</td>
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18
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh_auto_install</span>
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19
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">#</span>mkdir -p $(CURDIR)/debian/man</span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right">#asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_</span>src/*.adoc</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">#cp $(CURDIR)/debian/man_</span>src/*.? $(CURDIR)/debian/man</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/man</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> <span class="idiff left right">asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man</span>src/*.adoc</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">mv $(CURDIR)/debian/man</span>src/*.? $(CURDIR)/debian/man</span>
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24
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_installman --</span></pre>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#924314810df1cb51391abf924d0a92ec6f02374c"><strong>debian/vmatch.install</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">chain2dim</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#src/dist/vmatch/cleanpp.sh /usr/bin</span></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx"><span class="idiff left">src</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">dist</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">vmatch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">cleanpp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nx"><span class="idiff">sh</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">share</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff right">vmatch</span></span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">matchcluster</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mkdna6idx</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mkvtree</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vendian</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatchselect</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#src/dist/vmatch/vmigrate.sh /usr/bin</span></span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="nx"><span class="idiff left">src</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">dist</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">vmatch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">vmigrate</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nx"><span class="idiff">sh</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">share</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff right">vmatch</span></span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vseqinfo</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vseqselect</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dist</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vmatch</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vstree2tex</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<li id="57fac72d97fcc44b28a8e50d0ad4154c33ee48de">
<a href="https://salsa.debian.org/med-team/vmatch/compare/365ac97ac74d2f233fc20d2a5f9625b226a9d63c...d54735101a5a0a8a2fced27bef58e60540a1ed7b#57fac72d97fcc44b28a8e50d0ad4154c33ee48de"><strong>debian/vmatch.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/man/*.1</span></pre>
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