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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa">bfa1b2ff</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-13T13:57:05+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.2+dfsg</pre>
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<h4>7 changed files:</h4>
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.github/ISSUE_TEMPLATE/bug_report.md
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.github/ISSUE_TEMPLATE/feature_request.md
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.github/workflows/ccpp.yml
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.gitignore
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docs/html/jquery.js
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docs/latex/classsuffix__node.tex.tmp
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docs/latex/ivar_8cpp.tex.tmp
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<h4>Changes:</h4>
<li id="a03585ab89eed5e0782a1875b2d8153b97865d30">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa#a03585ab89eed5e0782a1875b2d8153b97865d30"><strong>.github/ISSUE_TEMPLATE/bug_report.md</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bug report</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="na" style="color: #008080;">about</span><span class="pi">:</span> <span class="s" style="color: #d14;">Create a report to help us improve</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" 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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<td class="diff-line-num new_line 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="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" 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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<td class="diff-line-num new_line 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="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Describe the bug**</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line 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="LC8" class="line" lang="markdown">A clear and concise description of what the bug is.</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**To Reproduce**</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">Steps to reproduce the behavior:</span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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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<td class="diff-line-num new_line 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="LC12" class="line" lang="markdown"><span class="p">1.</span> Go to '...'</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p">2.</span> Click on '....'</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">3.</span> Scroll down to '....'</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p">4.</span> See error</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" 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="markdown"><span class="gs" style="font-weight: 600;">**Expected behavior**</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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="LC18" class="line" lang="markdown">A clear and concise description of what you expected to happen.</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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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<td class="diff-line-num new_line 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="LC19" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="20" 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="LC20" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Screenshots**</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">If applicable, add screenshots to help explain your problem.</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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="LC22" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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="LC23" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Desktop (please complete the following information):**</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p"> -</span> OS: [e.g. iOS]</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p"> -</span> Browser [e.g. chrome, safari]</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="p"> -</span> Version [e.g. 22]</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Smartphone (please complete the following information):**</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="p"> -</span> Device: [e.g. iPhone6]</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p"> -</span> OS: [e.g. iOS8.1]</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="p"> -</span> Browser [e.g. stock browser, safari]</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="p"> -</span> Version [e.g. 22]</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Additional context**</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">Add any other context about the problem here.</span></pre>
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<li id="67c0231b0ea83057a5f5c051eb28641a29af34a6">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa#67c0231b0ea83057a5f5c051eb28641a29af34a6"><strong>.github/ISSUE_TEMPLATE/feature_request.md</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Feature request</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3
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<td class="diff-line-num new_line old" data-linenumber="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="markdown"><span class="na" style="color: #008080;">about</span><span class="pi">:</span> <span class="s" style="color: #d14;">Suggest an idea for this project</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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">
6
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<td class="diff-line-num new_line 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="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" 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">
7
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<td class="diff-line-num new_line 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="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Is your feature request related to a problem? Please describe.**</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line 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="LC8" class="line" lang="markdown">A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line 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="LC9" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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="LC10" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Describe the solution you'd like**</span></span>
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<td class="diff-line-num old old_line" 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="markdown">A clear and concise description of what you want to happen.</span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Describe alternatives you've considered**</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">A clear and concise description of any alternative solutions or features you've considered.</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Additional context**</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Add any other context or screenshots about the feature request here.</span></pre>
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<li id="bffe144f62bf1039a7711f6070e09a172eb81eac">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa#bffe144f62bf1039a7711f6070e09a172eb81eac"><strong>.github/workflows/ccpp.yml</strong>
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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;">C/C++ CI</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</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;">push</span><span class="pi">:</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;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</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;">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 class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"></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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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-linux</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>
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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;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</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="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line 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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-16.04</span><span class="pi">,</span> <span class="nv" style="color: #008080;">ubuntu-18.04</span><span class="pi">]</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"></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;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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@master</span></span>
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<pre style="margin: 0;">-<span id="LC20" 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;">download htslib</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz</span></span>
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22
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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;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">untar</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tar xf 1.10.2.tar.gz</span></span>
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24
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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;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">install htslib</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">-<span id="LC27" 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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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd htslib-1.10.2/</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="s" style="color: #d14;">autoheader</span></span>
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30
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<td class="diff-line-num new_line 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="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">autoconf</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="s" style="color: #d14;">./configure</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">make</span></span>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo make install</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo ldconfig</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" 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;">autotools</span></span>
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<td class="diff-line-num old old_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./autogen.sh</span></span>
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<td class="diff-line-num old old_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">-<span id="LC39" 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;">configure</span></span>
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<td class="diff-line-num old old_line" data-linenumber="40" 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">
40
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<td class="diff-line-num new_line 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="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="41" 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">
41
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<td class="diff-line-num new_line 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="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./configure</span></span>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">-<span id="LC43" 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;">make</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make</span></span>
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47
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<td class="diff-line-num new_line 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="LC47" 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;">make check</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make check</span></span>
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51
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<td class="diff-line-num new_line 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="LC51" 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;">make install</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="53" 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">
53
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<td class="diff-line-num new_line 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="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">CC</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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<td class="diff-line-num old old_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">sudo make install</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-macos</span><span class="pi">:</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml"></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">macos-latest</span> <span class="pi">]</span></span>
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59
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<td class="diff-line-num new_line 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="LC59" class="line" lang="yaml"></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">-<span id="LC61" 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@master</span></span>
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<td class="diff-line-num old old_line" data-linenumber="62" 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">
62
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<td class="diff-line-num new_line 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="LC62" 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 GNU autotools</span></span>
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<td class="diff-line-num old old_line" data-linenumber="63" 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">
63
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<td class="diff-line-num new_line 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="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">brew install autoconf automake libtool</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="64" 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">
64
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<td class="diff-line-num new_line 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="LC64" 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;">download htslib</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="65" 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">
65
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<td class="diff-line-num new_line 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="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">-<span id="LC66" 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;">untar</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="67" 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">
67
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<td class="diff-line-num new_line 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="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tar xf 1.10.2.tar.gz</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">-<span id="LC68" 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 htslib</span></span>
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<td class="diff-line-num old old_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">-<span id="LC69" 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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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd htslib-1.10.2/</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="s" style="color: #d14;">autoheader</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml"> <span class="s" style="color: #d14;">autoconf</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml"> <span class="s" style="color: #d14;">./configure</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml"> <span class="s" style="color: #d14;">make</span></span>
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<td class="diff-line-num old old_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo make install</span></span>
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<td class="diff-line-num old old_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">-<span id="LC76" 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;">autoconf</span></span>
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<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./autogen.sh</span></span>
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<td class="diff-line-num old old_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">-<span id="LC78" 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;">configure</span></span>
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<td class="diff-line-num old old_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">./configure</span></span>
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<td class="diff-line-num old old_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">-<span id="LC80" 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;">make</span></span>
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<td class="diff-line-num old old_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make</span></span>
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<td class="diff-line-num old old_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">-<span id="LC82" 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;">make check</span></span>
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<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">make check</span></span>
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<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">-<span id="LC84" 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;">make install</span></span>
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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">sudo make install</span></span></pre>
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<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*~</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.DS_Store</span>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">trim_primer_quality</span>
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4
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<td class="diff-line-num new_line 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="LC4" class="line" lang="plaintext">**/.snakemake/*</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">GPATH</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">GRTAGS</span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">GTAGS</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">*.pyc</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">**/.dSYM/*</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.dSYM/*</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">**/.deps/*</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">**/*.o</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Makefile</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">\hypertarget{classsuffix__node}{}\section{suffix\+\_\+node Class Reference}</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">\label{classsuffix__node}\index{suffix\+\_\+node@{suffix\+\_\+node}}</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Collaboration diagram for suffix\+\_\+node\+:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">% FIG 0</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">\subsection*{Public Member Functions}</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a8622127d06af65bd3d16ce5958995b1b}\label{classsuffix__node_a8622127d06af65bd3d16ce5958995b1b}} </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">{\bfseries suffix\+\_\+node} (int b, int $\ast$e, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$p, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$l)</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_ab465cab427de4e42b7b917e738b43425}\label{classsuffix__node_ab465cab427de4e42b7b917e738b43425}} </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">bool {\bfseries is\+\_\+leaf\+\_\+node} ()</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_af00dced817833c98c331293ebe819de5}\label{classsuffix__node_af00dced817833c98c331293ebe819de5}} </span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">bool {\bfseries contains\+\_\+child} (int ext)</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a7b47f09cf1d6a59849dba9fbcb1f3f61}\label{classsuffix__node_a7b47f09cf1d6a59849dba9fbcb1f3f61}} </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">int {\bfseries get\+\_\+length} ()</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a7fb5c818a596880ac914780e1b8c198f}\label{classsuffix__node_a7fb5c818a596880ac914780e1b8c198f}} </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">int {\bfseries get\+\_\+depth} ()</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a5469454f507f118785f65f206b141c3d}\label{classsuffix__node_a5469454f507f118785f65f206b141c3d}} </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">std\+::string {\bfseries get\+\_\+longest\+\_\+common\+\_\+substring} (std\+::string s1, std\+::string s2)</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_aec052c5cffdd951390cdfb40c360908e}\label{classsuffix__node_aec052c5cffdd951390cdfb40c360908e}} </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">std\+::string {\bfseries get\+\_\+path} (std\+::string s)</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a48933a8d9a3958c56dbbe98ae43deb84}\label{classsuffix__node_a48933a8d9a3958c56dbbe98ae43deb84}} </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">void {\bfseries extend\+\_\+path} (int $\ast$e)</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_af1c5aa14ccae896455815cd4c5a4d1a8}\label{classsuffix__node_af1c5aa14ccae896455815cd4c5a4d1a8}} </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries add\+\_\+child} (int ext, int b, int $\ast$e, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$l)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_ac25245d1931525b91678167fe07c4eb7}\label{classsuffix__node_ac25245d1931525b91678167fe07c4eb7}} </span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">void {\bfseries add\+\_\+child} (\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$c, int ext)</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a1ce4cfd4bf2136222a1162dd2555e2d3}\label{classsuffix__node_a1ce4cfd4bf2136222a1162dd2555e2d3}} </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries get\+\_\+child} (int ext)</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a50ab619252f0ad2091337bbf9688f9bf}\label{classsuffix__node_a50ab619252f0ad2091337bbf9688f9bf}} </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">bool {\bfseries contains\+\_\+depth} (int depth)</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a050ba7b3d5859d1dafb053e34a16663b}\label{classsuffix__node_a050ba7b3d5859d1dafb053e34a16663b}} </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">void {\bfseries print} (std\+::string s)</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a931f49a361496b16bfa52609ae82630d}\label{classsuffix__node_a931f49a361496b16bfa52609ae82630d}} </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">bool {\bfseries walk\+\_\+next} (int \&beg, int \&suffix\+\_\+length)</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">\end{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">\subsection*{Public Attributes}</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a9de4356329d9fd07511bcc4ee080df50}\label{classsuffix__node_a9de4356329d9fd07511bcc4ee080df50}} </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">int {\bfseries begin}</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a52e5a4ab12e08966e38db512ed6316dc}\label{classsuffix__node_a52e5a4ab12e08966e38db512ed6316dc}} </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">int {\bfseries nchildren}</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_af3d0857764f653e1a0f622af5215a4a0}\label{classsuffix__node_af3d0857764f653e1a0f622af5215a4a0}} </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">int $\ast$ {\bfseries end}</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_ac60ca6423a4769832874c1a6efe3d1c1}\label{classsuffix__node_ac60ca6423a4769832874c1a6efe3d1c1}} </span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$$\ast$ {\bfseries children}</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a3034292aaf83597ce658f45438c89133}\label{classsuffix__node_a3034292aaf83597ce658f45438c89133}} </span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries parent}</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">\mbox{\Hypertarget{classsuffix__node_a7d19dcd69e8b91ecbde055f7c4d86048}\label{classsuffix__node_a7d19dcd69e8b91ecbde055f7c4d86048}} </span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries suffix\+\_\+link}</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">\end{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">\item </span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">src/suffix\+\_\+tree.\+h\item </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">src/suffix\+\_\+tree.\+cpp\end{DoxyCompactItemize}</span></pre>
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<li id="cf9d70aa9e0a394c1b847bd6b7e9c73fcfafea03">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/bfa1b2ffea1bf6305475f4f7be2de15033db53fa#cf9d70aa9e0a394c1b847bd6b7e9c73fcfafea03"><strong>docs/latex/ivar_8cpp.tex.tmp</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">\hypertarget{ivar_8cpp}{}\section{src/ivar.cpp File Reference}</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">\label{ivar_8cpp}\index{src/ivar.\+cpp@{src/ivar.\+cpp}}</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">{\ttfamily \#include $<$iostream$>$}\newline</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">{\ttfamily \#include $<$unistd.\+h$>$}\newline</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}remove\+\_\+reads\+\_\+from\+\_\+amplicon.\+h\char`\"{}}\newline</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}call\+\_\+consensus\+\_\+pileup.\+h\char`\"{}}\newline</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}call\+\_\+variants.\+h\char`\"{}}\newline</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}trim\+\_\+primer\+\_\+quality.\+h\char`\"{}}\newline</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}get\+\_\+masked\+\_\+amplicons.\+h\char`\"{}}\newline</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">{\ttfamily \#include \char`\"{}suffix\+\_\+tree.\+h\char`\"{}}\newline</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Include dependency graph for ivar.\+cpp\+:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">% FIG 0</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">\subsection*{Classes}</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}}</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">\end{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">\subsection*{Functions}</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}\label{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}} </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">void {\bfseries print\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}\label{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}} </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">void {\bfseries print\+\_\+trim\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}\label{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}} </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">void {\bfseries print\+\_\+variants\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}\label{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}} </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">void {\bfseries print\+\_\+filtervariants\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}\label{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}} </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">void {\bfseries print\+\_\+consensus\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_afab6040035caaef89097988ea732ed2c}\label{ivar_8cpp_afab6040035caaef89097988ea732ed2c}} </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">void {\bfseries print\+\_\+removereads\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}\label{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}} </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">void {\bfseries print\+\_\+getmasked\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}\label{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}} </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">void {\bfseries print\+\_\+trimadapter\+\_\+usage} ()</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">int \mbox{\hyperlink{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}{main}} (int argc, char $\ast$argv\mbox{[}$\,$\mbox{]})</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">\end{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">\subsection*{Variables}</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">\begin{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}\label{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}} </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">const std\+::string {\bfseries V\+E\+R\+S\+I\+ON} = \char`\"{}1.\+0\char`\"{}</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">\item </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}\label{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}} </span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}} {\bfseries g\+\_\+args}</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">\end{DoxyCompactItemize}</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">\subsection{Function Documentation}</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">\mbox{\Hypertarget{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}\label{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}} </span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">\index{ivar.\+cpp@{ivar.\+cpp}!main@{main}}</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">\index{main@{main}!ivar.\+cpp@{ivar.\+cpp}}</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">\subsubsection{\texorpdfstring{main()}{main()}}</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">{\footnotesize\ttfamily int main (\begin{DoxyParamCaption}\item[{int}]{argc, }\item[{char $\ast$}]{argv\mbox{[}$\,$\mbox{]} }\end{DoxyParamCaption})}</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">Main Function</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">This is where the command line arguments into i\+Var are parsed. i\+Var first parses the first argument and depending on the command it either returns the version or uses G\+NU getopt to parse the remaining arguments. </span></pre>
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