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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqkit">Debian Med / seqkit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/abd67fc51c8d32ba1f7a04cc755aacf17b4a3b25">abd67fc5</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T15:46:36+00:00</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/seqkit/-/commit/ae9eb5c8cbb73b8b81f688e1db4e70791ed947b9">ae9eb5c8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T15:46:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing sources for repack bam files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/91a69c401714bffab1d60a2978ca317ba5a26dc3">91a69c40</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T15:47:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert to bam files during install
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/c1f42c1bc4b1e28a537d9c990e3fed7963f53c93">c1f42c1b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T15:48:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add new binary: seqkit-examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/620e910307418ba637a0882a732c9b3623c52466">620e9103</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T21:22:40+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
<span class="deleted-file">
−
debian/install
</span>
</a>
</li>
<li class="file-stats">
<a href="#0cc9de82b2c8447e620a7e90e00d1703c76f499c">
<span class="new-file">
+
debian/missing-sources/pcs109_5k.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#08b9522da2e656ec3428e45353ba50edcc216ba9">
<span class="new-file">
+
debian/missing-sources/pcs109_5k_prim.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#800f30abbcb3aab8d4db0a6edaa60cc61b48d7f5">
<span class="new-file">
+
debian/missing-sources/pcs109_5k_spliced.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#903a0c5a7f4e04a73e35b3bbaf758ffb2114bd3c">
<span class="new-file">
+
debian/seqkit-examples.docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#bdafd20230217a71b4d92cc4975a93f18cad22cf">
<span class="new-file">
+
debian/seqkit.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#fbc4a94942081747a74948e054c94834ececad91">
debian/links
→
debian/seqkit.links
</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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: seqkit</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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">
3
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-go</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6" 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="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
</pre>
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8
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-golang,</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +21,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> golang-github-op-go-logging-dev,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> golang-github-logrusorgru-aurora-dev,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> golang-github-tatsushid-go-prettytable-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="25" 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">
25
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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC25" class="line" lang="plaintext"> golang-github-bsipos-thist-dev</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> golang-github-bsipos-thist-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> samtools</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/seqkit</span>
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<td class="diff-line-num old_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/seqkit.git</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">@@ -43,3 +43,19 @@ Description: cross-platform and ultrafast toolkit for FASTA/Q file manipulation</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> demonstrates competitive performance in execution time and memory usage</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> compared to similar tools. The efficiency and usability of SeqKit enable</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> researchers to rapidly accomplish common FASTA/Q file manipulations.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Package: seqkit-examples</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Description: examples for seqkit: cross-platform and ultrafast toolkit for FASTA/Q file manipulation</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> SeqKit describes a cross-platform ultrafast comprehensive toolkit for</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> FASTA/Q processing. SeqKit provides executable binary files for all</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> major operating systems, including Windows, Linux, and Mac OS X, and can</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> be directly used without any dependencies or pre-configurations. SeqKit</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> demonstrates competitive performance in execution time and memory usage</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> compared to similar tools. The efficiency and usability of SeqKit enable</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> researchers to rapidly accomplish common FASTA/Q file manipulations.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> This package contains a test data set as well as sample scripts</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> running some test suite provided by Debian also as autopkgtest.</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">build/bin/seqkit usr/bin</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">build/bin/benchmark usr/lib/seqkit</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#0cc9de82b2c8447e620a7e90e00d1703c76f499c"><strong>debian/missing-sources/pcs109_5k.sam</strong></a>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#08b9522da2e656ec3428e45353ba50edcc216ba9"><strong>debian/missing-sources/pcs109_5k_prim.sam</strong></a>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#800f30abbcb3aab8d4db0a6edaa60cc61b48d7f5"><strong>debian/missing-sources/pcs109_5k_spliced.sam</strong></a>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#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">@@ -9,4 +9,13 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_auto_install:</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_auto_install -- --no-source</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> rm debian/seqkit/usr/bin/benchmark</span></pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> # Regenerate bam and bam index files</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> cat debian/missing-sources/pcs109_5k_spliced.sam | samtools view -Sb - > tests/pcs109_5k_spliced.bam</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> samtools index tests/pcs109_5k_prim.bam tests/pcs109_5k_prim.bam.bai</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh_installdocs</span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#903a0c5a7f4e04a73e35b3bbaf758ffb2114bd3c"><strong>debian/seqkit-examples.docs</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tests</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/missing-sources/*</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/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#bdafd20230217a71b4d92cc4975a93f18cad22cf"><strong>debian/seqkit.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">seqkit</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">benchmark</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">seqkit</span></span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#fbc4a94942081747a74948e054c94834ececad91"><strong>debian/links</strong>
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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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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/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>seqkit</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="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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<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="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-Rf</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-examples</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span>tests/hairpin.fa</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">seqkit <span class="nb" style="color: #0086b3;">seq</span> <span class="nt" style="color: #000080;">-w</span> 60 <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">></span> testfile</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 1"</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">filegrep</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'^>'</span> <span class="nv" style="color: #008080;">$file</span><span class="sb" style="color: #d14;">`</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nv" style="color: #008080;">testfilegrep</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'^>'</span> <span class="nv" style="color: #008080;">$file</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$filegrep</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="nv" style="color: #008080;">$testfilegrep</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">cksumfile</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$file</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s2" style="color: #d14;">" "</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="sb" style="color: #d14;">`</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">cksumtestfile</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cat </span>testfile | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">' '</span> <span class="nt" style="color: #000080;">-f</span> 1<span class="sb" style="color: #d14;">`</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 2"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" 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="nv" style="color: #008080;">$cksumfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cksumtestfile</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span></pre>
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