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<h3>
Andreas Tille pushed to branch upstream
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/5af791e2f29b16b2a87fc94ad4c5a3c225da354f">5af791e2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T14:39:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.5+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/c9ebde84f216da81f3458b03f0e40914fb8e6ce7">c9ebde84</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T14:59:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.5+dfsg</pre>
</li>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#8b09b55769c028063c592c342ad7e6b2689e6547">
<span class="deleted-file">
−
.github/workflows/c-cpp.yml
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
<span class="deleted-file">
−
.gitignore
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<li class="file-stats">
<a href="#d4f363b12339afef2d776bb54337618051dc0857">
base.cpp
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<li class="file-stats">
<a href="#a68dcf4bce8a71bb749a5f3379348905b07b28bb">
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+
test/mini-sorted.bam
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<li class="file-stats">
<a href="#51b30db44d1c3553ab8f363acd22e14f1337c3f2">
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+
test/mini-unsorted.bam
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<li class="file-stats">
<a href="#5a7b01a048b02cd9e988eaf93b4d6b3bef40ffdc">
test/test.sh
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<h4>Changes:</h4>
<li id="8b09b55769c028063c592c342ad7e6b2689e6547">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#8b09b55769c028063c592c342ad7e6b2689e6547"><strong>.github/workflows/c-cpp.yml</strong>
deleted
</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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2
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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>
</pre>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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4
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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>
</pre>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</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;">pull_request</span><span class="pi">:</span></span>
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7
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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>
</pre>
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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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9
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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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<td class="old_line diff-line-num old" data-linenumber="10" 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">
10
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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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<td class="old_line diff-line-num old" data-linenumber="11" 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">
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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<td class="old_line diff-line-num old" data-linenumber="14" 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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" 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="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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16
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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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<td class="old_line diff-line-num old" data-linenumber="17" 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="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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18
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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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19
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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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20
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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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<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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29
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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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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">flag.*</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">build.sh</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">a.out</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">*.bam.bai</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">mos*</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">.DS_Store</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">README.md~</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">exome</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">test_local</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">*.0.?</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">._*</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">*.sam</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">time.*</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">test2.bam</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">*.cpp~</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">*bak</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">pannelli</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">paper/paper.md~</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">TE</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">split_sam_by_flag.pl</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">mini_tests</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">.vscode</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">prova.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#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 1.3.<span class="idiff left right">1</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 1.3.<span class="idiff left right">5</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="diff-line-num unfold js-unfold old_line" data-linenumber="205" 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="205" 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">@@ -205,7 +205,7 @@ int main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-l"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--min-len"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MINLEN"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"print BED feature only if its length is bigger (or equal to) than MINLELN (default: %default)"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-z"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--min-ctg-len"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MINCTGLEN"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"Skip reference sequences (contigs) shorter than this value"</span><span class="p">);</span></span>
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207
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--discard-invalid-alignments"</span><span class="p">).</span><span class="n" style="color: #333;">action</span><span class="p">(</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"skip duplicates, failed QC, and non primary alignment, minq>0 (or user-defined if higher) (default: %default)"</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--keep-invalid-alignments"</span><span class="p">).</span><span class="n" style="color: #333;">action</span><span class="p">(</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"Keep duplicates, failed QC, and non primary alignment, min=0 (or user-defined if higher) (default: %default)"</span><span class="p">);</span></span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"></span>
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210
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// output options</span></span>
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211
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--output-strands"</span><span class="p">).</span><span class="n" style="color: #333;">action</span><span class="p">(</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"output coverage and stats separately for each strand"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" 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="216" 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">@@ -216,13 +216,34 @@ int main(int argc, char *argv[]) {</td>
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216
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">optparse</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Values</span> <span class="n" style="color: #333;">options</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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217
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></span>
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218
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">physical_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"physical_coverage"</span><span class="p">);</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">only_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"discard_invalid_alignments"</span><span class="p">);</span> </span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">only_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"discard_invalid_alignments"</span><span class="p">);</span> </span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep_invalid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"keep_invalid_alignments"</span><span class="p">);</span> </span>
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220
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <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;">minimum_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_cov"</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <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;">maximum_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"max_cov"</span><span class="p">);</span></span>
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <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;">minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_len"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <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;">minimum_contig_len</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_ctg_len"</span><span class="p">);</span></span>
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224
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_mapq"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// since 1.3.2 deprecate --discard-invalid-alignments</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_valid</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">keep_invalid</span><span class="p">)</span> <span class="p">{</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" 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;">"ERROR: --discard-invalid-alignments and --keep-invalid-alignments are incompatible."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"In the future --discard-invalid-alignments will be the default."</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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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <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;">only_valid</span> <span class="n" style="color: #333;">and</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">keep_invalid</span><span class="p">)</span> <span class="p">{</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" 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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234
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<pre style="margin: 0;">+<span id="LC234" 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;">"WARNING: --discard-invalid-alignments in the future will be activated by default."</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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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// only_valid = false by default as legacy behaviour</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_valid</span><span class="p">)</span> <span class="p">{</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" 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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239
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<pre style="margin: 0;">+<span id="LC239" 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;">"WARNING: --discard-invalid-alignments will be automatically enabled in the future."</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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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="p">}</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">only_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keep_invalid</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this if statement will remain: in the future only_valid will be the default</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">only_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="p">}</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_valid</span> <span class="n" style="color: #333;">and</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">min_mapq</span><span class="p">)</span> <span class="p">{</span></span>
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">min_mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" 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="285" 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">@@ -264,7 +285,14 @@ int main(int argc, char *argv[]) {</td>
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264
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"></span>
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265
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// output coverage</span></span>
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266
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">coverage_ends</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">coverage</span><span class="p">);</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check unsorted 1.3.4</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">next_change</span> <span class="p">)</span> <span class="p">{</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" 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;">"Position going backward, is the BAM sorted? last_pos="</span> <span class="o" style="font-weight: 600;">+</span> </span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">last_pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" next_change="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">next_change</span><span class="p">));</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="p">}</span></span>
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267
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">output</span><span class="p">({</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</span><span class="p">,</span> <span class="n" style="color: #333;">last_pos</span><span class="p">,</span> <span class="n" style="color: #333;">next_change</span><span class="p">},</span> <span class="n" style="color: #333;">coverage</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> </span>
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268
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"></span>
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269
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// increment coverage with alignments that start here</span></span>
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270
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">more_alignments_for_ref</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">next_change</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="317" 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">@@ -289,6 +317,8 @@ int main(int argc, char *argv[]) {</td>
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289
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"></span>
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290
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">debug</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[<] Coverage is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" from "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">next_change</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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291
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_change</span><span class="p">;</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"></span>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefLength</span><span class="p">);</span></span>
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293
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">debug</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[_] Completed at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [coverage:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">coverage_ends</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"]"</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="LC324" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reference ended</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">@@ -297,6 +327,7 @@ int main(int argc, char *argv[]) {</td>
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297
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327
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<pre style="margin: 0;"> <span id="LC327" 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;">"Try samtools fixmate on the input file"</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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298
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="p">}</span></span>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1.2.0 -- removed: assert(coverage_ends.empty());</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> </span>
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assert(!more_alignments);</span></span>
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">more_alignments</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#a68dcf4bce8a71bb749a5f3379348905b07b28bb"><strong>test/mini-sorted.bam</strong></a>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#51b30db44d1c3553ab8f363acd22e14f1337c3f2"><strong>test/mini-unsorted.bam</strong></a>
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<a href="https://salsa.debian.org/med-team/covtobed/-/compare/15f7e4d4050ff0c34c6ab978af2b527555068f60...c9ebde84f216da81f3458b03f0e40914fb8e6ce7#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">@@ -6,6 +6,7 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># REQUIRES: ./test/demo.bam</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ./test/mock.bam</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">COVTOBED_QUIET</span><span class="o" style="font-weight: 600;">=</span>1</span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">REMOVE</span><span class="o" style="font-weight: 600;">=</span>0</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"test/demo.bam"</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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11
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12
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<pre style="margin: 0;"> <span id="LC12" 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;">"WARNING: running this test from a bad location"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" 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">@@ -42,8 +43,24 @@ else</td>
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42
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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45
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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 class="c" style="color: #998; font-style: italic;"># Testing sortedness</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" 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;">" - Working with sorted file: "</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" 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>/mini-sorted.bam 2> /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FAIL"</span> <span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"FAIL"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" 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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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" 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;">" - Working with unsorted file (should raise error): "</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" 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>/mini-unsorted.bam 2> /dev/null <span class="o" style="font-weight: 600;">></span>/dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FAIL"</span> <span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"FAIL"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>PASS</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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47
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64
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<pre style="margin: 0;"> <span id="LC64" 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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48
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65
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<pre style="margin: 0;"> <span id="LC65" 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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49
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66
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<pre style="margin: 0;"> <span id="LC66" 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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