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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/allelecount">Debian Med / allelecount</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/385b4b73b46707b41e675dd128369f0d71a0afdf">385b4b73</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:36:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.2.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/abc39e7517f617d089a97aedd5dc4523f3ddb7bb">abc39e75</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:36:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/aec5af90cc44ec419dcd44cf65d483927ae6c40c">aec5af90</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:36:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.2.0'
Update to upstream version '4.2.0'
with Debian dir f768b94517fe5f4dbd1a5d5dabaf3c1858915a6f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/1c5e7e18fd492d43ea7be5c48b1b6becd59ffb13">1c5e7e18</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:36:26+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/allelecount/-/commit/41da495c3f487d97ec6e4140ed19fbd3feadb174">41da495c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:36:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/1192ebec65645b291a8ea20b305137bb63edce80">1192ebec</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-03T20:59:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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+
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#027f40d8d7bccd8caf08a7236885032f188780c1">
perl/lib/Sanger/CGP/AlleleCount.pm
</a>
</li>
<li class="file-stats">
<a href="#592a1aae25926e838f4bca2e1c8981f30b077dda">
setup.sh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># CHANGES</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## v4.2.0</span></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">
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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="markdown"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">*</span> Updated to hstlib 1.11</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## v4.1.0</span></span>
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="markdown"><span class="p">*</span> Created Docker file and build scripts to generate a containeraized code</span>
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</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">allelecount (4.2.0-1) 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"> * Team upload.</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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sat, 03 Oct 2020 20:36:32 +0530</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">allelecount (4.1.0-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Just use Build-Depends to enable build time testing</span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libconst-fast-perl <!nocheck>,</span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#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>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">CUR_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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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<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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/testData/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</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;">echo</span> <span class="s2" style="color: #d14;">"Testing C binary"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">alleleCounter <span class="nt" style="color: #000080;">-l</span> test10X.loci <span class="nt" style="color: #000080;">-b</span> test10X.bam <span class="nt" style="color: #000080;">-o</span> test1 <span class="nt" style="color: #000080;">-m</span> 2 <span class="nt" style="color: #000080;">-r</span> test10X.bam.bai</span>
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16
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<pre style="margin: 0;">+<span id="LC16" 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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test Perl counterpart"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">alleleCounter.pl <span class="nt" style="color: #000080;">-l</span> test10X.loci <span class="nt" style="color: #000080;">-b</span> test10X.bam <span class="nt" style="color: #000080;">-o</span> test2 <span class="nt" style="color: #000080;">-m</span> 2 <span class="nt" style="color: #000080;">-r</span> test10X.bam.bai</span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Check if both are same"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">diff <span class="nt" style="color: #000080;">-u</span> test1 test2</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;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test1 ./test2</span>
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25
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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;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span></pre>
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<li id="027f40d8d7bccd8caf08a7236885032f188780c1">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#027f40d8d7bccd8caf08a7236885032f188780c1"><strong>perl/lib/Sanger/CGP/AlleleCount.pm</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">@@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount;</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">base</span> <span class="p">'</span><span class="s1" style="color: #d14;">Exporter</span><span class="p">';</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">4.<span class="idiff left right">1</span>.0</span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">4.<span class="idiff left right">2</span>.0</span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@EXPORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw($VERSION)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="mi" style="color: #099;">1</span><span class="p">;</span></span></pre>
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<li id="592a1aae25926e838f4bca2e1c8981f30b077dda">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/de01c3599424c27358cb4daac8540b34c967ea3a...1192ebec65645b291a8ea20b305137bb63edce80#592a1aae25926e838f4bca2e1c8981f30b077dda"><strong>setup.sh</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">@@ -21,7 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">SOURCE_HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"https://github.com/samtools/htslib/releases/download/1.<span class="idiff left right">7/htslib-1.7</span>.tar.bz2"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">SOURCE_HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"https://github.com/samtools/htslib/releases/download/1.<span class="idiff left right">11/htslib-1.11</span>.tar.bz2"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="nv" style="color: #008080;">EXP_SAMV</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"1.3.1"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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