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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/covtobed">Debian Med / covtobed</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/15f7e4d4050ff0c34c6ab978af2b527555068f60">15f7e4d4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-03T21:01:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/8bc99d60754978efc418151b05a6544ab38b1fa1">8bc99d60</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-03T21:01:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.1+dfsg'
Update to upstream version '1.3.1+dfsg'
with Debian dir 14897f31f1c6667383ab680c7675149c5142bb68</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/45e38c4163fcdd8bbe71529a1851f3956d8d609f">45e38c41</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-03T21:22:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/5b871a5527ac9f9b0e8c5010b14a62e21b930957">5b871a55</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-03T21:22:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8b09b55769c028063c592c342ad7e6b2689e6547">
<span class="new-file">
+
.github/workflows/c-cpp.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#d4f363b12339afef2d776bb54337618051dc0857">
base.cpp
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#a53adf029254e0148bed48d71f6702649066310d">
debian/patches/test_use_system_installed_binary.patch
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<li class="file-stats">
<a href="#72a4c6294f757c90c4a0c0469471de2803404ac2">
<span class="new-file">
+
test/filt.bam
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</li>
<li class="file-stats">
<a href="#5da7861a8fb142d20fe12b54ad39626c9bd5854d">
<span class="new-file">
+
test/nano.bam
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<li class="file-stats">
<a href="#c79f428ab5e181cbdb8232cb64afde5be84a2101">
<span class="new-file">
+
test/stranded.bam
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<li class="file-stats">
<a href="#5a7b01a048b02cd9e988eaf93b4d6b3bef40ffdc">
test/test.sh
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</ul>
<h4>Changes:</h4>
<li id="8b09b55769c028063c592c342ad7e6b2689e6547">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#8b09b55769c028063c592c342ad7e6b2689e6547"><strong>.github/workflows/c-cpp.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">covtobed</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">on'</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">Build</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">${{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">matrix.os</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}'</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install dependencies (Ubuntu)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">runner.os == 'Linux'</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|-</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get update</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get install -y clang-3.9 g++-6 libbamtools-dev</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">[</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">$CXX</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">=</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">g++</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">]</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">export</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=g++-6</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">||</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">true'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">[</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">$CXX</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">=</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">clang++</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">]</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">export</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=clang++-3.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">||</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">true'</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">>-</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">g++ -std=c++11 *.cpp -I/usr/include/bamtools</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">/usr/lib/x86_64-linux-gnu/libbamtools.a -o covtobed -lz</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./covtobed -h</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./covtobed test/demo.bam > /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./covtobed --physical-coverage test/mp.bam > /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash test/test.sh</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</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;">gcc</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;">clang</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise-3.8</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-6</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.8</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">libbamtools-dev</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">[</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">$CXX</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">=</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">g++</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">]</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">export</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=g++-6</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">||</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">true"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">[</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">$CXX</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">=</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">clang++</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">]</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">export</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=clang++-3.8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">||</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">true"</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$CXX -std=c++11 *.cpp -I/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a -o covtobed -lz</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./covtobed -h</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./covtobed test/demo.bam > /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./covtobed --physical-coverage test/mp.bam > /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash test/test.sh</span></span></pre>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -3,8 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/vn/bioconda/covtobed?label=install%20from%20bioconda</span><span class="p">)</span>](http://bioconda.github.io/recipes/covtobed/README.html)</span>
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<td class="new_line diff-line-num" data-linenumber="5" 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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Bioconda installs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/covtobed</span><span class="p">)</span>](https://anaconda.org/bioconda/covtobed)</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![TravisCI Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/telatin/covtobed.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/telatin/covtobed)</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker build</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/pulls/andreatelatin/covtobed</span><span class="p">)</span>](https://hub.docker.com/r/andreatelatin/covtobed)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![covtobed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/telatin/covtobed/actions/workflows/c-cpp.yml/badge.svg</span><span class="p">)</span>](https://github.com/telatin/covtobed/actions/workflows/c-cpp.yml)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Codacy Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://app.codacy.com/project/badge/Grade/36944efb0d2b44cca850964e96c036a4</span><span class="p">)</span>](https://www.codacy.com/manual/telatin/covtobed?utm_source=github.com<span class="ni" style="color: #800080;">&</span>utm_medium=referral<span class="ni" style="color: #800080;">&</span>utm_content=telatin/covtobed<span class="ni" style="color: #800080;">&</span>utm_campaign=Badge_Grade)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b/status.svg</span><span class="p">)</span>](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b)</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -15,7 +14,7 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">Reads one (or more) <span class="p">[</span><span class="nv" style="color: #008080;">alignment</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/Sequence_alignment</span><span class="p">)</span> files</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">(sorted <span class="p">[</span><span class="nv" style="color: #008080;">BAM</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/SAM_(file_format</span><span class="p">)</span>)) and prints a <span class="p">[</span><span class="nv" style="color: #008080;">BED</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/BED_(file_format</span><span class="p">)</span>) with the <span class="p">[</span><span class="nv" style="color: #008080;">coverage</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.wikipedia.org/wiki/Coverage_(genetics</span><span class="p">)</span>). It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">:book: <span class="gs" style="font-weight: 600;">**[Read more in the wiki](https://github.com/telatin/covtobed/wiki)**</span> - this is the <span class="gs" style="font-weight: 600;">**main**</span> documentation source</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">:book: <span class="idiff left right"> </span><span class="gs" style="font-weight: 600;">**[Read more in the wiki](https://github.com/telatin/covtobed/wiki)**</span> - this is the <span class="gs" style="font-weight: 600;">**main**</span> documentation source</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">Features:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">*</span> Can read (sorted) BAMs from stream (like <span class="sb" style="color: #d14;">`bwa mem .. | samtools view -b | samtools sort - | covtobed`</span>)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,6 +100,12 @@ sudo docker run --rm -ti andreatelatin/covtobed coverage -h</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown">singularity <span class="nb" style="color: #0086b3;">exec </span>covtobed.simg coverage <span class="nt" style="color: #000080;">-h</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Startup message</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">When invoked without arguments, covtobed will print a message to inform the user that it</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown">is waiting for input from STDIN.</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown">To suppress this message, set the environment variable <span class="sb" style="color: #d14;">`COVTOBED_QUIET`</span> to <span class="sb" style="color: #d14;">`1`</span>.</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Performance</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*covtobed*</span> is generally faster than <span class="ge" style="font-style: italic;">*bedtools*</span>. More details are in the <span class="p">[</span><span class="nv" style="color: #008080;">benchmark</span><span class="p">](</span><span class="sx" style="color: #d14;">benchmark</span><span class="p">)</span> page.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,7 +137,7 @@ This program was finalized with a Flexible Talent Mobility Award funded by BBSRC</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown">If you use this tool, w<span class="idiff left">hy not citing the</span> paper<span class="idiff right">?</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">If you use this tool, w<span class="idiff left">e would really appreciate if you will cite its</span> paper<span class="idiff right">:</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Birolo et al., (2020). covtobed: a simple and fast tool to extract coverage tracks from BAM files. Journal of Open Source Software, 5(47), 2119, https://doi.org/10.21105/joss.02119</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"></span>
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<li id="d4f363b12339afef2d776bb54337618051dc0857">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#d4f363b12339afef2d776bb54337618051dc0857"><strong>base.cpp</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">@@ -16,7 +16,7 @@ using namespace std;</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DepthType</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// type for depth of coverage, kept it small</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ref_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// reference prefix for "counts" output</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%prog 1.<span class="idiff left right">2.0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%prog 1.<span class="idiff left right">3.1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Copyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="s" style="color: #d14;">"https://github.com/telatin/covtobed - License MIT"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,12 @@ class Input {</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">Input</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">paths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">),</span> <span class="n" style="color: #333;">discard_invalid_alignments</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paths</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// no input files, use standard input</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reading from STDIN... [try 'covtobed -h' for options]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1.3.0 - provide feedback unless $COVTOBED_QUIET is set to 1</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check environment variable COVTOBED_QUIET</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"COVTOBED_QUIET"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reading from STDIN... [Ctrl+C to exit; 'covtobed -h' for help]"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">input_bams</span><span class="p">.</span><span class="n" style="color: #333;">OpenFile</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"cannot read BAM from standard input, are you piping a BAM file?"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//throw input_bams.GetErrorString();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,6 +105,12 @@ struct Coverage {</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">equal</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Coverage</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stranded</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stranded</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Class for output handling: writes coverage in the specified format</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,7 +125,7 @@ class Output {</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// write interval to bed</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Interval</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Coverage</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// can the last interval be extended with the same coverage?</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last_interval</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last_interval</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">last_coverage</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last_interval</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last_interval</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">last_coverage</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">equal</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">strands</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// extend previous interval</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">last_interval</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">covtobed (1.3.1+dfsg-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"> * New upstream version 1.3.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Refresh patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Wed, 03 Nov 2021 21:09:46 +0530</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">covtobed (1.2.0+dfsg-2) unstable; urgency=medium</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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#a53adf029254e0148bed48d71f6702649066310d"><strong>debian/patches/test_use_system_installed_binary.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: modify test script so it works with autopkgtest</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-06-04</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- covtobed.orig/test/test.sh</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ covtobed/test/test.sh</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -7,40 +7,20 @@</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -7,38 +7,18 @@</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> # ./test/mock.bam</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> REMOVE=0</span>
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<td class="diff-line-num unfold js-unfold old_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>
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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">@@ -21,116 +17,137 @@ Last-Update: 2020-06-04</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [ `uname` == 'Darwin' ]; then</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " - Copying macOS binary" || echo " ERROR: pre-compiled binary not working"</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp ./binaries/covtobed_mac ./covtobed</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version<span class="idiff left right"> >/dev/null || echo " ERROR: pre-compiled binary not working"</span></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " - Trying Ubuntu binary"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp ./binaries/covtobed ./covtobed</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version || echo " ERROR: pre-compiled binary not working"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covtobed --version <span class="idiff left right">>/dev/null </span>|| echo " ERROR: pre-compiled binary not working"</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed --version</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed --version</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> echo " ================================================ "</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> set -eou pipefail</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> # Compilation success, checking that --version emits the expected "progname" string</span>
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37
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> echo -n " - Compiled binary prints version: "</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --version | grep covtobed | wc -l ) -<span class="idiff left right">eq</span> "1" ];</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --version | grep covtobed | wc -l ) -<span class="idiff left right">eq</span> "1" ];</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --version | grep covtobed | wc -l ) -<span class="idiff left right">gt</span> "1" ];</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --version | grep covtobed | wc -l ) -<span class="idiff left right">gt</span> "1" ];</span></span>
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40
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> then</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> echo PASS 1</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo PASS $(./covtobed --version | grep covtobed |head -n 1)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo PASS $(covtobed --version | grep covtobed |head -n 1)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> else</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo FAIL $(./covtobed --version | grep covtobed | wc -l )</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo FAIL $(covtobed --version | grep covtobed | wc -l )</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> exit</span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -46,7 +26,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)</span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> echo -n " - Minimum coverage, expected BED lines check: "</span>
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46
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 15 test/demo.bam | wc -l) -eq "12" ];</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 15 <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>demo.bam | wc -l) -eq "12" ];</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 15 demo.bam | wc -l) -eq "12" ];</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> then</span>
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49
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> echo PASS 2</span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> else</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="p">@@ -5<span class="idiff left">0</span>,7 +3<span class="idiff right">0</span>,7 @@</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -5<span class="idiff left">6</span>,7 +3<span class="idiff right">6</span>,7 @@</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> </span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> # Checking thath --physical-coverage will work, and it fits the expected number of lines</span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> echo -n " - Physical coverage, expected BED lines check: "</span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --physical-coverage test/mp.bam | wc -l) -eq "136" ];</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --physical-coverage <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>mp.bam | wc -l) -eq "136" ];</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --physical-coverage mp.bam | wc -l) -eq "136" ];</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> then</span>
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58
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> echo PASS 3</span>
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59
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> else</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">0</span>,7 +4<span class="idiff right">0</span>,7 @@</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">6</span>,7 +4<span class="idiff right">6</span>,7 @@</span></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> </span>
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62
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> # Checking stranded output: it should produce content in the fifth column of the bed file</span>
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63
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> echo -n " - Stranded output, testing column #5: "</span>
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64
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --out test/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --out <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --out demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];</span></span>
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66
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> then</span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> echo PASS 4</span>
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68
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> else</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left">0</span>,7 +5<span class="idiff right">0</span>,7 @@</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left">6</span>,7 +5<span class="idiff right">6</span>,7 @@</span></span>
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70
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> </span>
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71
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> # Checking the "counts" output (counting the lines containing a ">")</span>
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72
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> echo -n " - Testing 'counts' format (printed headers): "</span>
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73
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --format counts test/demo.bam | grep '>' | wc -l) -eq "2" ];</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>demo.bam | grep '>' | wc -l) -eq "2" ];</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts demo.bam | grep '>' | wc -l) -eq "2" ];</span></span>
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75
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> then</span>
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76
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> echo PASS 5</span>
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77
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> else</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">78,7 +58,7</span> @@</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">84,29 +64,29</span> @@</span></span>
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79
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> exit 1</span>
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80
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> fi</span>
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81
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> echo -n " - Testing 'counts' format (printed lines): "</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --format counts test/demo.bam | grep -v <span class="idiff left right">'>'</span> | wc -l) -eq "202" ];</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts <span class="idiff left">/usr/share/doc/covtobed-examples/examples/</span>demo.bam | grep -v <span class="idiff right">'>'</span> | wc -l) -eq "202" ];</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed --format counts test/demo.bam | grep -v <span class="idiff left right">\></span> | wc -l) -eq "202" ];</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed --format counts demo.bam | grep -v <span class="idiff left right">\></span> | wc -l) -eq "202" ];</span></span>
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84
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> then</span>
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85
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> echo PASS 6</span>
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86
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> else</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="p">@@ -88,11 +68,11 @@</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> exit 1</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> fi</span>
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88
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> echo -n " - Testing strand with adjacent intervals: "</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ $(./covtobed test/stranded.bam | wc -l) -eq "1" && $(./covtobed --output-strands test/stranded.bam | wc -l) -eq "2" ]];</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [[ $(covtobed stranded.bam | wc -l) -eq "1" && $(covtobed --output-strands stranded.bam | wc -l) -eq "2" ]];</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> then</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> echo PASS 7</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> else</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> exit 1</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> fi</span>
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89
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> # Checking BED output with reference output file</span>
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90
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> echo -n " - Checking identity of BED output with pre-calculated: "</span>
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91
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed test/demo.bam > test/output.test</span></span>
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92
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>demo.bam > output.test</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>output.bed | wc -l) -eq "0" ];</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed demo.bam > output.test</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test output.bed | wc -l) -eq "0" ];</span></span>
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95
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> then</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"> echo PASS <span class="idiff left right">7</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> echo PASS <span class="idiff left right">8</span></span>
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97
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm test/output.test</span></span>
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98
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm output.test</span></span>
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99
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> else</span>
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100
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> echo FAIL</span>
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101
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> exit 1</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">00</span>,11 +<span class="idiff right">80</span>,11 @@</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">14</span>,11 +<span class="idiff right">94</span>,11 @@</span></span>
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103
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> </span>
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104
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> ## Synthetic BAM test</span>
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105
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"> echo -n " - Checking computed coverage for a synthetic BAM file: "</span>
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106
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed -m 1 test/mock.bam > test/output.test</span></span>
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107
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed -m 1 <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>mock.bam > output.test</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>mock.bed | wc -l) -eq "0" ];</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed -m 1 mock.bam > output.test</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(diff output.test mock.bed | wc -l) -eq "0" ];</span></span>
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110
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> then</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"> echo PASS <span class="idiff left right">8</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> echo PASS <span class="idiff left right">9</span></span>
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112
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm test/output.test</span></span>
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113
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm output.test</span></span>
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114
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> else</span>
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115
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> echo FAIL</span>
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116
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"> exit 1</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">1</span>2,23 +<span class="idiff right">92</span>,23 @@</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left">6</span>,23 +<span class="idiff right">106</span>,23 @@</span></span>
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118
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> </span>
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119
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> ## Filter non valid alignments</span>
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120
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> echo -n " - Checking filtering of invalid alignments: "</span>
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121
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 -d <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>filtered.bam | wc -l) -eq "2" ] ; then</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"> echo -n "PASS <span class="idiff left right">9</span>,"</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 -d filtered.bam | wc -l) -eq "2" ] ; then</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> echo -n "PASS <span class="idiff left right">10</span>,"</span>
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124
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="diff"> else</span>
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125
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="diff"> echo FAIL</span>
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126
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"> exit 1</span>
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127
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> fi</span>
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128
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ $(./covtobed -m 1 test/filtered.bam | wc -l) -eq "6" ] ; then</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>filtered.bam | wc -l) -eq "6" ] ; then</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ $(covtobed -m 1 filtered.bam | wc -l) -eq "6" ] ; then</span></span>
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130
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff"> echo 10</span>
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131
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> else</span>
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132
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "FAIL: $(./covtobed -m 1 -d test/filtered.bam | wc -l)"</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "FAIL: $(covtobed -m 1 -d <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>filtered.bam | wc -l)"</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "FAIL: $(covtobed -m 1 -d filtered.bam | wc -l)"</span></span>
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="diff"> exit 1</span>
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135
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="diff"> fi</span>
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136
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" 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="155" 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">@@ -138,15 +155,14 @@ Last-Update: 2020-06-04</td>
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138
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"> # covered exactly {n}X times</span>
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139
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"> echo " - Checking artificial coverage values:"</span>
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140
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-./covtobed test/test_cov.bam -m 1 |cut -f 1,4| while read LINE;</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed <span class="idiff left right">/usr/share/doc/covtobed-examples/examples/</span>test_cov.bam -m 1 |cut -f 1,4| while read LINE;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+covtobed test_cov.bam -m 1 |cut -f 1,4| while read LINE;</span></span>
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142
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> do</span>
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143
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> echo "$LINE" | perl -ne '($exp, $cov)=split /\s+/, $_; if ("$exp" ne "${cov}X") {</span>
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144
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> die "$exp != $cov\n";</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="p">@@ -137,7 +117,3 @@</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"> }'</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"> done</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -153,5 +133,5 @@</span></span>
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148
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"> echo "ALL TESTS: PASSED"</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span></span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>if [[ $REMOVE -eq 1 ]]; then</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="idiff left right"> </span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="idiff left right"> </span>if [[ $REMOVE -eq 1 ]]; then</span>
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151
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm ./covtobed</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span></pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm covtobed</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> fi</span></pre>
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<li id="72a4c6294f757c90c4a0c0469471de2803404ac2">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#72a4c6294f757c90c4a0c0469471de2803404ac2"><strong>test/filt.bam</strong></a>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#5da7861a8fb142d20fe12b54ad39626c9bd5854d"><strong>test/nano.bam</strong></a>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#c79f428ab5e181cbdb8232cb64afde5be84a2101"><strong>test/stranded.bam</strong></a>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957#5a7b01a048b02cd9e988eaf93b4d6b3bef40ffdc"><strong>test/test.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">@@ -20,24 +20,30 @@ if [ ! -e "./covtobed" ]; then</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span><span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'Darwin'</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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21
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21
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<pre style="margin: 0;"> <span id="LC21" 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;">" - Copying macOS binary"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ERROR: pre-compiled binary not working"</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> ./binaries/covtobed_mac ./covtobed</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> covtobed <span class="nt" style="color: #000080;">--version</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> covtobed <span class="nt" style="color: #000080;">--version</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff">/dev/null </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff right">" ERROR: pre-compiled binary not working"</span></span></span>
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24
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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;">else</span></span>
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25
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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;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" - Trying Ubuntu binary"</span></span>
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26
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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;">cp</span> ./binaries/covtobed ./covtobed</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"> covtobed <span class="nt" style="color: #000080;">--version</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ERROR: pre-compiled binary not working"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> covtobed <span class="nt" style="color: #000080;">--version</span> <span class="o" style="font-weight: 600;"><span class="idiff left">></span></span><span class="idiff right">/dev/null </span><span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ERROR: pre-compiled binary not working"</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell">./covtobed <span class="nt" style="color: #000080;">--version</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ================================================ "</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-eou</span> pipefail</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Compilation success, checking that --version emits the expected "progname" string</span></span>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Compiled binary prints version: "</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--version</span> | <span class="nb" style="color: #0086b3;">grep </span>covtobed | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span> <span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">eq</span></span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></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> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--version</span> | <span class="nb" style="color: #0086b3;">grep </span>covtobed | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span> <span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-<span class="idiff left right">gt</span></span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS 1</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--version</span> | <span class="nb" style="color: #0086b3;">grep </span>covtobed |head <span class="nt" style="color: #000080;">-n</span> 1<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--version</span> | <span class="nb" style="color: #0086b3;">grep </span>covtobed | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span> <span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Minimum coverage, expected BED lines check: "</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">-m</span> 15 <span class="nb" style="color: #0086b3;">test</span>/demo.bam | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"12"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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">@@ -78,20 +84,28 @@ else</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Testing 'counts' format (printed lines): "</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--format</span> counts <span class="nb" style="color: #0086b3;">test</span>/demo.bam | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="s1" style="color: #d14;"><span class="idiff left right">'>'</span></span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"202"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--format</span> counts <span class="nb" style="color: #0086b3;">test</span>/demo.bam | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="se" style="color: #d14;"><span class="idiff left right">\></span></span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"202"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS 6</span>
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84
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL<span class="idiff left"> </span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="idiff">./covtobed </span><span class="nt" style="color: #000080;"><span class="idiff">--format</span></span><span class="idiff"> counts </span><span class="nb" style="color: #0086b3;"><span class="idiff">test</span></span><span class="idiff">/demo.bam | </span><span class="nb" style="color: #0086b3;"><span class="idiff">grep</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="se" style="color: #d14;"><span class="idiff">\></span></span><span class="idiff"> | </span><span class="nb" style="color: #0086b3;"><span class="idiff">wc</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-l</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="idiff right"> when 202 expected</span></span>
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86
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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87
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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88
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Testing strand with adjacent intervals: "</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nb" style="color: #0086b3;">test</span>/stranded.bam | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--output-strands</span> <span class="nb" style="color: #0086b3;">test</span>/stranded.bam | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"2"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS 7</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">--format</span> counts <span class="nb" style="color: #0086b3;">test</span>/demo.bam | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> <span class="se" style="color: #d14;">\></span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> when 202 expected</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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89
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Checking BED output with reference output file</span></span>
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90
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<td class="new_line diff-line-num" data-linenumber="104" 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">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Checking identity of BED output with pre-calculated: "</span></span>
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91
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="shell">./covtobed <span class="nb" style="color: #0086b3;">test</span>/demo.bam <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">test</span>/output.test</span>
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92
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>diff <span class="nb" style="color: #0086b3;">test</span>/output.test <span class="nb" style="color: #0086b3;">test</span>/output.bed | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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93
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS <span class="idiff left right">7</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS <span class="idiff left right">8</span></span>
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95
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm test</span>/output.test</span>
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96
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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97
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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="117" 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">@@ -103,7 +117,7 @@ echo -n " - Checking computed coverage for a synthetic BAM file: "</td>
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103
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell">./covtobed <span class="nt" style="color: #000080;">-m</span> 1 <span class="nb" style="color: #0086b3;">test</span>/mock.bam <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">test</span>/output.test</span>
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104
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>diff <span class="nb" style="color: #0086b3;">test</span>/output.test <span class="nb" style="color: #0086b3;">test</span>/mock.bed | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="105" 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">
105
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" 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">
106
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<td class="new_line diff-line-num old" data-linenumber="120" 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="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS <span class="idiff left right">8</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS <span class="idiff left right">9</span></span>
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107
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm test</span>/output.test</span>
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108
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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109
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" 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="127" 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">@@ -113,7 +127,7 @@ fi</td>
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113
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Filter non valid alignments</span></span>
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114
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" - Checking filtering of invalid alignments: "</span></span>
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<td class="old_line diff-line-num" data-linenumber="115" 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">
115
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span>./covtobed <span class="nt" style="color: #000080;">-m</span> 1 <span class="nt" style="color: #000080;">-d</span> <span class="nb" style="color: #0086b3;">test</span>/filtered.bam | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-eq</span> <span class="s2" style="color: #d14;">"2"</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="old_line diff-line-num old" data-linenumber="116" 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">
116
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<td class="new_line diff-line-num old" data-linenumber="130" 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="LC116" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"PASS <span class="idiff left right">9</span>,"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="130" 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">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"PASS <span class="idiff left right">10</span>,"</span></span>
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117
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num" data-linenumber="118" 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">
118
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<td class="new_line diff-line-num" data-linenumber="132" 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">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>FAIL</span>
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<td class="old_line diff-line-num" data-linenumber="119" 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">
119
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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