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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/abacas">Debian Med / abacas</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/964a94ab83ac271f17abba20746521a1b85f4a7a">964a94ab</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:20:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/dc8f7cc81ac4d71c60bf6f3b250b948af8b64d31">dc8f7cc8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:21:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add relevant examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/137eb52623aceac74d7e398e645b3bfe7b40ea2f">137eb526</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:28:47+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/e468c6aea0e242b37e1555bc5ae5a412365cae7d">e468c6ae</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:29:13+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump compat version to 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/9e706a80d7426f3a1b77acdc8b79163c7401a027">9e706a80</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:29:37+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add "Rules-Requires-Root:no"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/27fef2c4f4311c3cd91c4f0080ea9de3091a0da8">27fef2c4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T19:33:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ee547bf1edd41582defb0a446ecaa9d4c9d81586">
debian/abacas.1
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#14fea0078728545f6a156de7c63df9f8ed927ef8">
<span class="new-file">
+
debian/tests/README
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8b339fbeeb793a71557763a24132d1d7ff6f6095">
<span class="new-file">
+
debian/tests/data/454AllContigs.fna
</span>
</a>
</li>
<li class="file-stats">
<a href="#607bcbfb1aee9ba5de3725ad4fb0e4d23022e50a">
<span class="new-file">
+
debian/tests/data/SS_SC84.dna
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ee547bf1edd41582defb0a446ecaa9d4c9d81586">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#ee547bf1edd41582defb0a446ecaa9d4c9d81586"><strong>debian/abacas.1</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,9 +16,7 @@ reference sequence in a single fasta file</td>
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<td class="diff-line-num old_line" data-linenumber="16" 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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<td class="diff-line-num new_line" data-linenumber="16" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">\fIqs\fR</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">contigs in multi\-fasta format</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">\fI\prog\fR</span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">MUMmer program to use: 'nucmer' or 'promer'</span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">MUMmer program to use 'nucmer' or 'promer'</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" 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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<td class="diff-line-num new_line" data-linenumber="20" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" 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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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">\fIpsf\fR</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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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<td class="diff-line-num new_line" data-linenumber="22" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">pseudomolecule/ordered sequence file in fasta format</span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: abacas</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Nilesh Patra <npatra974@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/abacas</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/abacas.git</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://abacas.sourceforge.net/</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: abacas</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: all</span>
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<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#14fea0078728545f6a156de7c63df9f8ed927ef8"><strong>debian/tests/README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests for abacas</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The data for tests has been referenced from:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> https://www.sanger.ac.uk/resources/downloads/bacteria/streptococcus-suis.html</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<li id="8b339fbeeb793a71557763a24132d1d7ff6f6095">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#8b339fbeeb793a71557763a24132d1d7ff6f6095"><strong>debian/tests/data/454AllContigs.fna</strong></a>
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<li id="607bcbfb1aee9ba5de3725ad4fb0e4d23022e50a">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#607bcbfb1aee9ba5de3725ad4fb0e4d23022e50a"><strong>debian/tests/data/SS_SC84.dna</strong></a>
The diff for this file was not included because it is too large.
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>abacas</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 1'</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">abacas <span class="nt" style="color: #000080;">-r</span> SS_SC84.dna <span class="nt" style="color: #000080;">-q</span> 454AllContigs.fna <span class="nt" style="color: #000080;">-p</span> nucmer <span class="nt" style="color: #000080;">-f</span> 150 <span class="nt" style="color: #000080;">-l</span> 70 <span class="nt" style="color: #000080;">-V</span> 3 <span class="nt" style="color: #000080;">-b</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 2'</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">abacas <span class="nt" style="color: #000080;">-r</span> SS_SC84.dna <span class="nt" style="color: #000080;">-q</span> 454AllContigs.fna <span class="nt" style="color: #000080;">-p</span> nucmer <span class="nt" style="color: #000080;">-i</span> 80 <span class="nt" style="color: #000080;">-v</span> 30 <span class="nt" style="color: #000080;">-N</span> <span class="nt" style="color: #000080;">-m</span> <span class="nt" style="color: #000080;">-c</span></span></pre>
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