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<h3>
Tony Mancill pushed to branch debian-950311
at <a href="https://salsa.debian.org/med-team/fastqc">Debian Med / fastqc</a>
</h3>
<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/-/commit/939c0d47d17bda57c64e0a215f834015ea41585e">939c0d47</a></strong>
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<span>by tony mancill</span>
<i>at 2020-04-06T15:30:51-07:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update debian/source/include-binaries after renaming test file
Gbp-Dch: ignore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/-/commit/88efed4269c0875f8478d7f9aab136467ce4156b">88efed42</a></strong>
<div>
<span>by tony mancill</span>
<i>at 2020-04-06T15:56:42-07:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Exit non-zero after test failure and adjust location of tests_dir
Gbp-Dch: ignore
</pre>
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<h4>2 changed files:</h4>
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<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<a href="https://salsa.debian.org/med-team/fastqc/-/compare/f68b71eb1c85d7f273221f408fcfbca7140c1d85...88efed4269c0875f8478d7f9aab136467ce4156b#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.fastqc/toy.bam</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests.fastqc/toy<span class="idiff left right">_bam</span>.bam</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/fastqc/-/compare/f68b71eb1c85d7f273221f408fcfbca7140c1d85...88efed4269c0875f8478d7f9aab136467ce4156b#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"fastqc"</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">test<span class="idiff left">_dir</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$PWD</span></span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">test<span class="idiff left">s_dir</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$PWD</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/debian/tests</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">test_failures</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC8" 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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ find . -name "*.gz" -exec gunzip \{\} \;</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>sample <span class="k" style="font-weight: 600;">in </span>example.fastq toy_sam.sam toy_bam.bam <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> /usr/bin/fastqc <span class="nt" style="color: #000080;">--extract</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"> <span class="nv" style="color: #008080;">result</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">sample</span><span class="p">%%.*</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_fastqc"</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="nv" style="color: #008080;">expected</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">test_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">result</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_expected_summary.txt"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nv" style="color: #008080;">expected</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">test<span class="idiff left right">s</span>_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">result</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_expected_summary.txt"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> diff <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">result</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/summary.txt"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">expected</span><span class="k" style="font-weight: 600;">}</span> 2>/dev/null <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="o" style="font-weight: 600;">((</span> test_failures +<span class="o" style="font-weight: 600;">=</span> 1 <span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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>
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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">@@ -36,6 +36,8 @@ done</td>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span> test_failures <span class="o" style="font-weight: 600;">==</span> 0 <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="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FAIL mismatched fastqc summary count: </span><span class="nv" style="color: #008080;">$test_failures</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FAIL mismatched fastqc summary count: </span><span class="nv" style="color: #008080;">$test_failures</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit </span>1</span></pre>
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