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<h3>
Shruti Sridhar pushed to branch master
at <a href="https://salsa.debian.org/med-team/spaced">Debian Med / spaced</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/-/commit/921df8d20bbc60e74dbe821ab5cd2223cddcdb31">921df8d2</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-22T21:21:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add test data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/-/commit/298e48a0cdce36e8754084f4c0b8088ea2888671">298e48a0</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-22T21:22:14+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/spaced/-/commit/9842f2b56a7284fb1c05a93094d3ed148dcbc086">9842f2b5</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-22T21:22:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/-/commit/0b545da4584465e42958e6b7d8278fad4a7b3e38">0b545da4</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-22T21:24:09+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
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</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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</a>
</li>
<li class="file-stats">
<a href="#e3c65a84430335d49d160a3ca56f8d83126edf39">
<span class="new-file">
+
debian/tests/data/pattern
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</li>
<li class="file-stats">
<a href="#73f426412088fc36eff83b9bcbd77465a09d3b85">
<span class="new-file">
+
debian/tests/data/sequence.fasta
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span>
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<td class="new_line diff-line-num new" 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>
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<td class="new_line diff-line-num new" 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="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">testing</span> </span>
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<td class="new_line diff-line-num new" 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="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<td class="new_line diff-line-num new" 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="nc" style="color: #458; font-weight: 600;">Files</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">/*</span></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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="php"><span class="nc" style="color: #458; font-weight: 600;">The</span> <span class="n" style="color: #333;">test</span> <span class="nf" style="color: #900; font-weight: 600;">files</span> <span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">fasta</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">patter</span><span class="p">)</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">written</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span><span class="mf" style="color: #099;">.</span> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="php"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spaced (1.2.0-201605+dfsg-3) UNRELEASED; urgency=medium</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"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add test data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Thu, 22 Jul 2021 21:23:23 +0530</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">spaced (1.2.0-201605+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,10 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: © 2016 Fabian Klötzl <kloetzl@evolbio.mpg.de></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: GPL-3+</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">Files: debian/tests/data</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Copyright: © 2020 Shruti Sridhar <shruti.sridhar99@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: GPL-3+</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">Files: debian/patches/0003-Add-autotools-buildsystem.patch</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Copyright: 2008 Benjamin Kostnik <bkoz@redhat.com>,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> 2012 Zack Weinberg <zackw@panix.com>,</span>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#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/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#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></pre>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#e3c65a84430335d49d160a3ca56f8d83126edf39"><strong>debian/tests/data/pattern</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">11001</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#73f426412088fc36eff83b9bcbd77465a09d3b85"><strong>debian/tests/data/sequence.fasta</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>AT1G00001|1|test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ATGCCGATGACTAGACTAGACATAGACATA</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">GGGAATAGACATAGACATAGAGCATAGACA</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">GATAGAGAGAACAGATAGACACACATAGACA</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">CACAG</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/-/compare/f3a625f1c0a8ec440a3948dd9324e7dde4ac3ec2...0b545da4584465e42958e6b7d8278fad4a7b3e38#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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2
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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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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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>spaced</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" 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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">spaced <span class="nt" style="color: #000080;">-o</span> output <span class="nt" style="color: #000080;">-f</span> pattern sequence.fasta </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"output"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Pass Test"</span></span></pre>
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