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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-rainbow">Debian Med / bio-rainbow</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/f7f6d38823881911cbb9ac158b2e237f7e68b49b">f7f6d388</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:14:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install data for autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/8ca3ff307e5393119741ea5a7d8337d82b992967">8ca3ff30</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:14:33+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/bio-rainbow/-/commit/dd7e3e909e2a46d25a30ec71f3f400aef8a5c8fe">dd7e3e90</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:19:01+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/bio-rainbow/-/commit/194fc3e80e594f6a6a9e97baed2309261d4c815b">194fc3e8</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:26:29+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Pranav Ballaney to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/9917fe5bf37d0167db0d037380b6da598b461564">9917fe5b</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:29:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/fa54a5d5fd0eb5487be3c18d99c0ba8958973ce0">fa54a5d5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:29:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/11cca782149255936e06328b8118572003956382">11cca782</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:29:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/539ec9d997efdeb9e274d7db9534b0a8e2fb71ec">539ec9d9</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:30:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Remove trailing whitespace in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/2a82325966399cf60588bc11ccf597cac8dd6c51">2a823259</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:30:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/9f803384c473e01eb23904d4f994115b92454150">9f803384</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:30:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/61d31d448bce8373f886f5d1f3b4928c2843baae">61d31d44</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:31:35+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/-/commit/aeea114a055c708f06d01bd398f0f122e02710ea">aeea114a</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-23T05:32:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>13 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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<span class="new-file">
+
debian/source/include-binaries
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#ac10590a1297326a92e8f9a4538db450286053d7">
<span class="new-file">
+
debian/tests/data/R.1.fastq.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#40e3388f1e5102780956d11aeb189a704843adbd">
<span class="new-file">
+
debian/tests/data/R.2.fastq.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">the</span> <span class="nx">files</span> <span class="nx">used</span> <span class="k" style="font-weight: 600;">for</span> <span class="nx">testing</span> <span class="nx">this</span> <span class="nx">package</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">─────────────────────────────────────────────────</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" 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 class="nx">R</span><span class="o" style="font-weight: 600;">.</span><span class="mf" style="color: #099;">1.</span><span class="nx">fasta</span> <span class="k" style="font-weight: 600;">and</span> <span class="nx">R</span><span class="o" style="font-weight: 600;">.</span><span class="mf" style="color: #099;">2.</span><span class="nx">fasta</span> <span class="nx">were</span> <span class="nx">generated</span> <span class="k" style="font-weight: 600;">as</span> <span class="nx">random</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="php"><span class="nx">sequences</span><span class="p">,</span> <span class="nx">using</span> <span class="nx">rangen</span> <span class="nx">from</span> <span class="nx">dazzdb</span> <span class="k" style="font-weight: 600;">and</span> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="php"><span class="nx">artfastqgenerator</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">following</span> <span class="nx">commands</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="php"> <span class="nx">rangen</span> <span class="mf" style="color: #099;">0.005</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">r2020</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">R</span><span class="o" style="font-weight: 600;">.</span><span class="nx">fasta</span> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="php"> <span class="nx">artfastqgenerator</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">O</span> <span class="nx">R</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">R</span> <span class="nx">R</span><span class="o" style="font-weight: 600;">.</span><span class="nx">fasta</span> <span class="o" style="font-weight: 600;">-</span><span class="nx">S</span> <span class="s2" style="color: #d14;">">random"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-rainbow (2.0.4+dfsg-2) unstable; 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"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Updated bio.tools ref</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Added ref to conda</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Install data for autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add Pranav Ballaney to Uploaders</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</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"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sun, 23 Aug 2020 05:32:47 +0530</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">bio-rainbow (2.0.4+dfsg-1) unstable; urgency=medium</span>
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2
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: bio-rainbow</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Olivier Sallou <osallou@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 13</span>),</span>
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7
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> help2man</span>
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8
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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9
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git</span>
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11
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/bio-rainbow/</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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12
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: bio-rainbow</span>
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14
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">README.txt</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">README.txt</span></pre>
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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/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#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/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -10,7 +10,7 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</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">%:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> dh $@<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> # dh_installman is messing up .sh extension as language extension</span>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/R.1.fastq.gz</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/data/R.2.fastq.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#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/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#ac10590a1297326a92e8f9a4538db450286053d7"><strong>debian/tests/data/R.1.fastq.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/-/compare/20c752433a34bb10020f6a903a0bbe446cf5eb3a...aeea114a055c708f06d01bd398f0f122e02710ea#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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3
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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>bio-rainbow</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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">bio-rainbow cluster <span class="nt" style="color: #000080;">-1</span> R.1.fastq <span class="nt" style="color: #000080;">-2</span> R.2.fastq <span class="o" style="font-weight: 600;">></span> rbcluster.out 2> log</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">bio-rainbow div <span class="nt" style="color: #000080;">-i</span> rbcluster.out <span class="nt" style="color: #000080;">-o</span> rbdiv.out</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">bio-rainbow merge <span class="nt" style="color: #000080;">-o</span> rbasm.out <span class="nt" style="color: #000080;">-a</span> <span class="nt" style="color: #000080;">-i</span> rbdiv.out <span class="nt" style="color: #000080;">-N50000</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"4f0a35450f64adc3bfd6f4b664887631 rbasm.out"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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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;">"29a755de547ac393328c8b31d5f6e26d rbcluster.out"</span> <span class="o" style="font-weight: 600;">>></span> checksums</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;">"b7dfd0cfd2f0eade15487a72632e972d rbdiv.out"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span></pre>
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