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<h3>
Shruti Sridhar pushed to branch master
at <a href="https://salsa.debian.org/med-team/ea-utils">Debian Med / ea-utils</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/4e7f198aa75ccff53bd10bdb0605ae45994ec7c1">4e7f198a</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-08-04T17:36:12+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/ea-utils/-/commit/1b0c9fb5cb101d7196d0bd949e4ae7f0ed8ec530">1b0c9fb5</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-08-04T17:36:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add get-test-data script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ea-utils/-/commit/1332ed8e842b187255ff856509cb0c39b04c8fe6">1332ed8e</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-08-04T17:37:35+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/ea-utils/-/commit/bad9f826a1f76e0112fe9512c1d4c876e2874528">bad9f826</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-08-04T17:37:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
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</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
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="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
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+
debian/source/include-binaries
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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</li>
<li class="file-stats">
<a href="#3b7eb6cab874201f0fe71695602d4ba6c9dc8813">
<span class="new-file">
+
debian/tests/data/adapters.fa
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<li class="file-stats">
<a href="#f5231f7af1c674ac6c02a3f66521836ff0cda468">
<span class="new-file">
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debian/tests/data/data.fastq.gz
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</li>
<li class="file-stats">
<a href="#0e9418a52713c2cf65a28de530bba2247ab2237f">
<span class="new-file">
+
debian/tests/get-test-data
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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/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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1
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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>
</pre>
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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">
2
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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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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="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>
</pre>
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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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<td class="new_line diff-line-num new" 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="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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<td class="new_line diff-line-num new" 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>
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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 class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></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;">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="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="nc" style="color: #458; font-weight: 600;">Source</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">https</span><span class="o" style="font-weight: 600;">://</span><span class="n" style="color: #333;">trace</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">ncbi</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">nlm</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">nih</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">gov</span><span class="o" style="font-weight: 600;">/</span><span class="nc" style="color: #458; font-weight: 600;">Traces</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sra</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sra</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">cgi</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">exp</span><span class="o" style="font-weight: 600;">=</span><span class="no" style="color: #008080;">SRX11266476</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">search</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">downloads</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seq</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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"></span>
</pre>
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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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">First</span> <span class="mi" style="color: #099;">100</span> <span class="n" style="color: #333;">lines</span> <span class="n" style="color: #333;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">fastq</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">taken</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">adapter</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">fa</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="LC14" class="line" lang="php"></span>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#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 +14,10 @@ Copyright: © 2011 Erik Aronesty <erik@q32.com></td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> 2010 Illumina, Inc</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">License: MIT</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">Files: debian/tests/data/*</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Copyright: NCBI </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">License: PD</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Files: razf.c</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Copyright: 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">License: BSD-2-clause</span>
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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">@@ -78,3 +82,24 @@ License: MIT</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> THE SOFTWARE.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">License: PD</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> PUBLIC DOMAIN NOTICE</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> National Center for Biotechnology Information</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> This software/database is a "United States Government Work" under the</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> terms of the United States Copyright Act. It was written as part of</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> the author's official duties as a United States Government employee and</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> thus cannot be copyrighted. This software/database is freely available</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> to the public for use. The National Library of Medicine and the U.S.</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> Government have not placed any restriction on its use or reproduction.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> .</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> Although all reasonable efforts have been taken to ensure the accuracy</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> and reliability of the software and data, the NLM and the U.S.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> Government do not and cannot warrant the performance or results that</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> may be obtained by using this software or data. The NLM and the U.S.</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> Government disclaim all warranties, express or implied, including</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> warranties of performance, merchantability or fitness for any particular</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> purpose.</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> .</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> Please cite the author in any work or product based on this material.</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/get-test-data</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/data.fastq.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#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/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#3b7eb6cab874201f0fe71695602d4ba6c9dc8813"><strong>debian/tests/data/adapters.fa</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>adapters</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ATGCTACGCATCGACTACGAC</span></pre>
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<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#f5231f7af1c674ac6c02a3f66521836ff0cda468"><strong>debian/tests/data/data.fastq.gz</strong></a>
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1
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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>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Needs fastq-dump from the SRA toolkit to directly get the 100 raw fastq reads</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">fastq-dump <span class="nt" style="color: #000080;">-X</span> 100 <span class="nt" style="color: #000080;">-Z</span> SRR14953521 | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n100</span> <span class="o" style="font-weight: 600;">></span> data.fastq</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> data</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></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;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> data/data.fastq.gz <span class="o" style="font-weight: 600;">]</span></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;">then</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>data/data.fastq.gz</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">diff <span class="nt" style="color: #000080;">-u</span> data.fastq data/data.fastq</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$?</span><span class="sb" style="color: #d14;">`</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" 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;">"The data has changed, injecting new data, please check manually before upload"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" 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">
18
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<pre style="margin: 0;">+<span id="LC18" 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;">"The data is same, no changes needed"</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;">fi</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;">fi</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gzip </span>data.fastq</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>data/data.fastq</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv </span>data.fastq.gz data/data.fastq.gz</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Done"</span></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ea-utils/-/compare/6d0022757c1489c8eeb0f40e0d08188b1f462cb7...bad9f826a1f76e0112fe9512c1d4c876e2874528#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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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>ea-utils</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"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">fastq-mcf adapters.fa data.fastq.gz <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">fastq-stats data.fastq.gz <span class="o" style="font-weight: 600;">></span> statistics</span>
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<pre style="margin: 0;">+<span id="LC19" 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;">"statistics"</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 class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS tests"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> </span></pre>
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