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<h3>
Shruti Sridhar pushed to branch master
at <a href="https://salsa.debian.org/med-team/blasr">Debian Med / blasr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/ba610e322cb50abcc5324cdc4fd21838c1c93a6a">ba610e32</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-31T23:19:28+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/blasr/-/commit/0d6a57efbadc0761ea51b94672ffa261d0479986">0d6a57ef</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-31T23:19:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/65276bd00ee42fda9bfae89d5416db5455ff224f">65276bd0</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-07-31T23:20:04+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
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</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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debian/examples
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
<a href="#22c65213cfa756557b33ab839468c78a5bc5db4c">
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debian/tests/data/query.fasta
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<li class="file-stats">
<a href="#0621768541f66261c3ccdebade9959d428fa36cd">
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debian/tests/data/ref.fa
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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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">
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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>
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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>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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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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<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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<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>
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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="n" style="color: #333;">files</span> <span class="n" style="color: #333;">query</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;">ref</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">fa</span> <span class="n" style="color: #333;">were</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></pre>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#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">@@ -14,6 +14,9 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Copyright: 2015-2016 Afif Elghraoui <afif@debian.org></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">License: PacBio-BSD-3-Clause</span>
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16
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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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Files: debian/tests/data</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Copyright: Shruti Sridhar <shruti.sridhar99@gmail.com></span>
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19
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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">License: PacBio-BSD-3-Clause</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> modification, are permitted provided that the following conditions</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">README*</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README.md</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/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#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/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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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/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#22c65213cfa756557b33ab839468c78a5bc5db4c"><strong>debian/tests/data/query.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>movie/0/0_64</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ATGTCAGTGACGATGACAGTAGACAGATAGAGAGGAGAGATAGACAGATAG</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#0621768541f66261c3ccdebade9959d428fa36cd"><strong>debian/tests/data/ref.fa</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>test/0/0_68</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ATGTCAGTGACGATGACAGTAGACAGATAGAGAGGAGAGATAGACAGATAGATGCTAGC</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/81f260d916c71b9d655dd3781a3b527d5cca0fa0...65276bd00ee42fda9bfae89d5416db5455ff224f#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>blasr</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">blasr query.fasta ref.fa <span class="nt" style="color: #000080;">--sam</span> <span class="nt" style="color: #000080;">--out</span> alignment.sam</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">blasr query.fasta ref.fa <span class="nt" style="color: #000080;">--minMatch</span> 1 <span class="nt" style="color: #000080;">--maxMatch</span> 10 <span class="o" style="font-weight: 600;">></span> output</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"amd64"</span> <span class="o" style="font-weight: 600;">]</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"8db2f4d5737a90d087da90a6779c8d7b output"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"0a61b96282acbc63df897dd1510ea0ad alignment.sam"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Expected output and generated output are same: PASS Test"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"alignment.sam"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS Test"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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