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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/genomethreader">Debian Med / genomethreader</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/af89066afe6788c9a3e1255fbcb6dd45c90b44ec">af89066a</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-10T16:57:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do not install gthunit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/8f9242003322dbb2c50a2e04c9f60762a7cc76b2">8f924200</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-10T16:57:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">finish patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/077c0c8678e847890bf269ce97c23d0727e51704">077c0c86</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-10T16:58:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/5992651908887879d83f52128d75cf4a0947ac4f">59926519</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-10T16:58:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add more manpages
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d13b548a5ae920ecafb8265c79f7e10224fe0c94">
debian/genomethreader.install
</a>
</li>
<li class="file-stats">
<a href="#4503df8507ce925a4f22ca460fc68e7ad645d662">
<span class="new-file">
+
debian/man_src/gthbssmfileinfo.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#8334e09a4e716b6bfbebdd9ad1b67c215bc27001">
<span class="new-file">
+
debian/man_src/gthbssmprint.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#74761eb9c292e5c3cb9f75d0e1a42df2e478812c">
<span class="new-file">
+
debian/man_src/gthbssmrmsd.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#ff99f2bc14d34fc305e81613ea36e7a4d9809ac4">
<span class="new-file">
+
debian/man_src/gthbssmtrain.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#16e482caef09aa73ce6a9c7c0ac63b5d683cc6e5">
<span class="new-file">
+
debian/man_src/gthconsensus.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#082a178a6c3726765809589970e53ce06bce2dab">
<span class="new-file">
+
debian/man_src/gthfilestat.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#6c687bb4255c067ef3653d2fe4548ecb4aa56951">
<span class="new-file">
+
debian/man_src/gthgetseq.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#cbdf7b4ff026406d37fce5d9122073fbad185fcd">
<span class="new-file">
+
debian/man_src/gthmkbssmfiles.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6568c6387c78858b96b05382fbe1234c9738040">
<span class="new-file">
+
debian/man_src/gthsplit.1.adoc
</span>
</a>
</li>
<li class="file-stats">
<a href="#f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
debian/patches/debian-gt-libs.patch
</a>
</li>
<li class="file-stats">
<a href="#411b0a9c431115faa7f24dda94d08f1855b28c1b">
debian/patches/gt-path-fix.patch
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<span class="new-file">
+
debian/patches/hardening.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="d13b548a5ae920ecafb8265c79f7e10224fe0c94">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#d13b548a5ae920ecafb8265c79f7e10224fe0c94"><strong>debian/genomethreader.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">bin</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>
</pre>
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1
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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="LC1" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">align_dna</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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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="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gth</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthbssmfileinfo</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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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">
4
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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="LC4" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthbssmrmsd</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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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="LC5" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthconsensus</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthgetseq</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthsplit</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthbssmbuild</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthbssmprint</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthbssmtrain</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthfilestat</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthmkbssmfiles</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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<td class="diff-line-num new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bssm</span> <span class="nx">usr</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">genomethreader</span></span>
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3
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">gthdata</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">genomethreader</span></span></pre>
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<li id="4503df8507ce925a4f22ca460fc68e7ad645d662">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#4503df8507ce925a4f22ca460fc68e7ad645d662"><strong>debian/man_src/gthbssmfileinfo.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthbssmfileinfo(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">gthbssmfileinfo - show info about splice site model</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">*gthbssmfileinfo* [option ...] bssm_file</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">Show information about the specified BSSM file.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</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">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> display help and exit</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#8334e09a4e716b6bfbebdd9ad1b67c215bc27001"><strong>debian/man_src/gthbssmprint.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthbssmprint(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">gthbssmprint - print splice site model</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">*gthbssmprint* [option ...] bssm_file</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">Print BSSM file bssm_file to stdout.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</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">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> display help and exit</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#74761eb9c292e5c3cb9f75d0e1a42df2e478812c"><strong>debian/man_src/gthbssmrmsd.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthbssmrmsd(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">gthbssmrmsd - calculate distance between splice site models</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">*gthbssmrmsd* [option ...] BSSM_file_1 BSSM_file_2</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">Show RMSDs between given BSSM files.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</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">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> display help and exit</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#ff99f2bc14d34fc305e81613ea36e7a4d9809ac4"><strong>debian/man_src/gthbssmtrain.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthbssmtrain(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">gthbssmtrain - train splice site model</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">*gthbssmtrain* [option ...] GFF3_file</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">Create BSSM training data from annotation given in GFF3_file.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">*-outdir*::</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> set name of output directory to which the training files are</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> written</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> default: training_data</span>
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21
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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">*-gcdonor*::</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> extract training data for GC donor sites</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> default: yes</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">*-filtertype*::</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> set type of features to used for filtering (usually 'exon' or</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> 'CDS')</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> default: exon</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">*-goodexoncount*::</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> set the minimum number of good exons a feature must have to be</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> included into the training data</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> default: 1</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">*-cutoff*::</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> set the minimum score an exon must have to count towards the</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ``good exon count'' (exons without a score count as good)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> default: 1.00</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">*-extracttype*::</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> set type of features to be extracted as exons (usually 'exon' or</span>
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<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
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> 'CDS')</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> default: CDS</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">*-seqfile*::</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> set the sequence file from which to take the sequences</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> default: undefined</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">*-encseq*::</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> set the encoded sequence indexname from which to take the</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> sequences</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> default: undefined</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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">*-seqfiles*::</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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> set the sequence files from which to extract the features</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> use '--' to terminate the list of sequence files </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">*-matchdesc*::</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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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> search the sequence descriptions from the input files for the</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> desired sequence IDs (in GFF3), reporting the first match</span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> default: no</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">*-matchdescstart*::</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> exactly match the sequence descriptions from the input files for</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> the desired sequence IDs (in GFF3) from the beginning to the</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> first whitespace</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> default: no</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">*-usedesc*::</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> use sequence descriptions to map the sequence IDs (in GFF3) to</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> actual sequence entries.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> If a description contains a sequence range (e.g.,</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> III:1000001..2000000), the first part is used as sequence ID</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> ('III') and the first range position as offset ('1000001')</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> default: no</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">*-regionmapping*::</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> set file containing sequence-region to sequence file mapping</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> default: undefined</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">*-seed*::</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> set seed for random number generator manually</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> 0 generates a seed from the current time and the process id</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> default: 0</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">*-v*::</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> be verbose</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> default: no</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">*-gzip*::</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> write gzip compressed output files</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> default: no</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">*-bzip2*::</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> write bzip2 compressed output files</span>
</pre>
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97
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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="LC97" class="line" lang="plaintext"> default: no</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"></span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">*-force*::</span>
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100
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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="LC100" class="line" lang="plaintext"> force writing to output files</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> default: no</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">*-help*::</span>
</pre>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> display help and exit</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">*-version*::</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> display version information and exit</span></pre>
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<li id="16e482caef09aa73ce6a9c7c0ac63b5d683cc6e5">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#16e482caef09aa73ce6a9c7c0ac63b5d683cc6e5"><strong>debian/man_src/gthconsensus.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthconsensus(1)</span>
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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">## 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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">gthconsensus - build consensus spliced alignments</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>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*gthconsensus* [option ...] [file ...]</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
</pre>
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11
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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">Show GenomeThreader output files containing intermediate results and assemble</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">the contained spliced alignments to consensus spliced alignments.</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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17
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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">*-translationtable*::</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> set the codon translation table used for codon translation in</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> matching, DP, and output</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> default: 1</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">*-v*::</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> be verbose</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> default: no</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">*-xmlout*::</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> show output in XML format</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> default: no</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">*-gff3out*::</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> show output in GFF3 format</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> default: no</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">*-md5ids*::</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> show MD5 fingerprints as sequence IDs</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> default: no</span>
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<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
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
</pre>
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<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
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">*-o*::</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="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
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> redirect output to specified 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="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"> default: undefined</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="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"></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="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">*-gzip*::</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="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"> write gzip compressed output file</span>
</pre>
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</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="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"> default: no</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="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>
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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="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">*-bzip2*::</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="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"> write bzip2 compressed output 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="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"> default: no</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="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"></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="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">*-force*::</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="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"> force writing to output 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="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"> default: no</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"></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">*-gs2out*::</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"> output in old GeneSeqer2 format</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="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"> default: no</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">*-minalignmentscore*::</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"> set the minimum alignment score for spliced alignments to be</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"> included into the set of spliced alignments</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"> default: 0.00</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"></span>
</pre>
</td>
</tr>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">*-maxalignmentscore*::</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> set the maximum alignment score for spliced alignments to be</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> default: 1.00</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">*-mincoverage*::</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> set the minimum coverage for spliced alignments to be</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> included into the set of spliced alignments</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> default: 0.00</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">*-maxcoverage*::</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> set the maximum coverage for spliced alignments to be</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> included into the set of spliced alignments</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> default: 9999.99</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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<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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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">*-intermediate*::</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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> stop after calculation of spliced alignments and output</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="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> results in reusable XML format. Do not process this output</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> yourself, use the ``normal'' XML output instead!</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> default: no</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" 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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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> display help for basic options and exit</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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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"></span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" 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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> display help for all options and exit</span>
</pre>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#082a178a6c3726765809589970e53ce06bce2dab"><strong>debian/man_src/gthfilestat.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthfilestat(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">gthfilestat - show statistics about consensus spliced alignments</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">*gthfilestat* [option ...] [file ...]</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">Show statistics about spliced alignments in GenomeThreader output files</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">containing intermediate results.</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">*-minalignmentscore*::</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> set the minimum alignment score for spliced alignments to be</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> default: 0.00</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">*-maxalignmentscore*::</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> set the maximum alignment score for spliced alignments to be</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> default: 1.00</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">*-mincoverage*::</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> set the minimum coverage for spliced alignments to be</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> default: 0.00</span>
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32
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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">*-maxcoverage*::</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> set the maximum coverage for spliced alignments to be</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> default: 9999.99</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">*-v*::</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> be verbose</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> default: no</span>
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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">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> display help and exit</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#6c687bb4255c067ef3653d2fe4548ecb4aa56951"><strong>debian/man_src/gthgetseq.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthgetseq(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">gthgetseq - get FASTA sequences from GenomeThreader files</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">*gthgetseq* -getcdna | -getprotein | -getgenomic [option ...] [file ...]</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>
</pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Get FASTA sequences from GenomeThreader files containing intermediate results.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The sequences are shown on stdout.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">## OPTIONS</span>
</pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">*-getcdna*::</span>
</pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> get cDNA/EST sequences</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> default: no</span>
</pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">*-getcdnacomp*::</span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> get complement of cDNA/EST sequences</span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> default: no</span>
</pre>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">*-getprotein*::</span>
</pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> get protein sequences</span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> default: no</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">*-getproteincomp*::</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> get complement of protein sequences</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> default: no</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">*-getgenomic*::</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> get genomic sequences</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> default: no</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">*-getgenomiccomp*::</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> get complement of genomic sequences</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> default: no</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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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">*-minalignmentscore*::</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> set the minimum alignment score for spliced alignments to be</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> default: 0.00</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">*-maxalignmentscore*::</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> set the maximum alignment score for spliced alignments to be</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> default: 1.00</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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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">*-mincoverage*::</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> set the minimum coverage for spliced alignments to be</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> default: 0.00</span>
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56
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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">*-maxcoverage*::</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> set the maximum coverage for spliced alignments to be</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> default: 9999.99</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">*-gzip*::</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> gzip compressed input file(s)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> default: no</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">*-bzip2*::</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> bzip2 compressed input file(s)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> default: no</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">*-help*::</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> display help and exit</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">*-version*::</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> display version information and exit</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#cbdf7b4ff026406d37fce5d9122073fbad185fcd"><strong>debian/man_src/gthmkbssmfiles.1.adoc</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthmkbssmfiles(1)</span>
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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">## 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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">gthmkbssmfiles - rite hard coded BSSM files</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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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">*gthmkbssmfiles* output_path</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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12
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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">Write hard coded BSSM files to output_path.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</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">*-help*::</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> display help and exit</span>
</pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">*-version*::</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> display version information and exit</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#d6568c6387c78858b96b05382fbe1234c9738040"><strong>debian/man_src/gthsplit.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gthsplit(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">gthsplit - split GenomeThreader output files</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">*gthsplit* -alignmentscore | -coverage [option ...] [file ...]</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Split GenomeThreader output files containing intermediate results.</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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">## OPTIONS</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">*-alignmentscore*::</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> split according to the overall alignment score (scr)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> default: no</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">*-coverage*::</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> split according to coverage (cov)</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> default: no</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">*-range*::</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> set the percentage range used to create the sets</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> default: 5</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">*-minalignmentscore*::</span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> set the minimum alignment score for spliced alignments to be</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> included into the set of spliced alignments</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> default: 0.00</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">*-maxalignmentscore*::</span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> set the maximum alignment score for spliced alignments to be</span>
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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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> included into the set of spliced alignments</span>
</pre>
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<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
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> default: 1.00</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="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
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<pre style="margin: 0;">+<span id="LC38" 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="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
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">*-mincoverage*::</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="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
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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="LC40" class="line" lang="plaintext"> set the minimum coverage for spliced alignments to be</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="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
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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="LC41" class="line" lang="plaintext"> included into the set of spliced alignments</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="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"> default: 0.00</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="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
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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="LC43" 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="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
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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="LC44" class="line" lang="plaintext">*-maxcoverage*::</span>
</pre>
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<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="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"> set the maximum coverage for spliced alignments to be</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="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"> included into the set of spliced alignments</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="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"> default: 9999.99</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="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"></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="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">*-v*::</span>
</pre>
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</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="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"> be verbose</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="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"> default: no</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="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">*-gzip*::</span>
</pre>
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</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"> write gzip compressed output file(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="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"> default: no</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"></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">*-bzip2*::</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"> write bzip2 compressed output file(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="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"> default: no</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"></span>
</pre>
</td>
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<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">*-force*::</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> force writing to split files</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> default: no</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">*-help*::</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> display help and exit</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">*-version*::</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> display version information and exit</span>
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<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
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span></pre>
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<li id="f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#f19f900306f42aafd11c9c6fd4e4e288988b9c4a"><strong>debian/patches/debian-gt-libs.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: use Debian's GenomeTools</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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1
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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3
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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="diff"><span class="p">@@ -15,19 +15,17 @@</span></span>
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<li id="411b0a9c431115faa7f24dda94d08f1855b28c1b">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#411b0a9c431115faa7f24dda94d08f1855b28c1b"><strong>debian/patches/gt-path-fix.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: use Debian's gt path</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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1
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/testsuite/gthbssmtrain_include.rb</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/testsuite/gthbssmtrain_include.rb</span></span>
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3
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span></span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Enable full hardening</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -229,7 +229,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(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="LC6" class="line" lang="diff"> $(1): $(2)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="diff"> @echo "[link $$(@F)]"</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> @test -d $$(@D) || mkdir -p $$(@D)</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $$(CC) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $$(CC) $$(CPPFLAGS) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="diff"> $$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="diff"> $$(EXP_LDLIBS)) $$(OVERRIDELIBS) -o $$@</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> endef</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -319,7 +319,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> $(1): $(2)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> @echo "[compile $$(@F)]"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> @test -d $$(@D) || mkdir -p $$(@D)</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $$(CC) $$(CPPFLAGS) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> $$(GTH_CFLAGS) $(3)</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="diff"> $$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> $(3) -MM -MP -MT $$@</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">debian-gt-libs.patch</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">gt-path-fix.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">hardening.patch</span></pre>
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