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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libbioparser-dev">Debian Med / libbioparser-dev</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/714586ed227a00c73bbc27bc5fe9a7bff9ce1268">714586ed</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:08:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/58dccf73ed064f18637c24f264f98e0ab900a468">58dccf73</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:08:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.15</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/50e06d56fb66efc4e413f5054a00b019e27862b4">50e06d56</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:08:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/75737d51c31b913eb44c7dd8ab810892998ce8d6">75737d51</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:08:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.0.15'
Update to upstream version '3.0.15'
with Debian dir ecc2aac829a17e0d9cece45a869c50b9e91242e4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/4c26c6a2b3357344595437eb52997317500b5d8a">4c26c6a2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:08:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7">1b77cbd3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-15T08:44:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: libbiosoup-dev
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#852d3ffb1f5efe9b870bdb4af4a8e7a61b3a3a3e">
<span class="new-file">
+
.github/workflows/bioparser.yml
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<li class="file-stats">
<a href="#9e1a62480721ea8da8e2bc6a6c3cf9d790767f2d">
include/bioparser/fastq_parser.hpp
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<li class="file-stats">
<a href="#ba35fbe579108bcc7bd6117bebf894744989f40a">
include/bioparser/parser.hpp
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<h4>Changes:</h4>
<li id="852d3ffb1f5efe9b870bdb4af4a8e7a61b3a3a3e">
<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#852d3ffb1f5efe9b870bdb4af4a8e7a61b3a3a3e"><strong>.github/workflows/bioparser.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">bioparser CI</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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">BUILD_TYPE</span><span class="pi">:</span> <span class="s" style="color: #d14;">Release</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang++</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang++-4.0</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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25
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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;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler == 'g++-4.8' }}</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup GCC</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">egor-tensin/setup-gcc@v1</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">4.8"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">platform</span><span class="pi">:</span> <span class="s" style="color: #d14;">x64</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler == 'clang++-4.0' }}</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup Clang</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">egor-tensin/setup-clang@v1</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">4.0"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">platform</span><span class="pi">:</span> <span class="s" style="color: #d14;">x64</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" 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 CMake</span></span>
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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;">cmake -B ${{ github.workspace }}/build -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">CXX</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler }}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC46" 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;">Build</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">working-directory</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ github.workspace }}/build</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">bin/bioparser_test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
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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;">matrix</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;">include</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="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GCC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4.8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># GCC 4.8.5 & CMake 3.12.4</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;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</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;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</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;">apt</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;">sources</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</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;">packages</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="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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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;">SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.5</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 3.5.2 & CMake 3.12.4</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;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">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;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</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;">apt</span><span class="pi">:</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.5</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Xcode</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">9.4</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(OSX)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 9.4.1 & CMake 3.15.5</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode9.4</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${SET_COMPILER}"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build && cd build</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release .. && make</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./bin/bioparser_test</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.11<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bioparser VERSION 3.0.1<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bioparser VERSION 3.0.1<span class="idiff left right">5</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"> LANGUAGES CXX</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"> DESCRIPTION <span class="s2" style="color: #d14;">"Bioparser is a c++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Bioparser</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Latest GitHub release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/rvaser/bioparser.svg</span><span class="p">)</span>](https://github.com/rvaser/bioparser/releases/latest)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;">![Build status for gcc/clang</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff">travis-ci</span>.com/rvaser/bioparser<span class="idiff">.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.com/rvaser/bioparser</span>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Build status for gcc/clang</span><span class="p">](</span><span class="sx" style="color: #d14;">https://<span class="idiff left">github</span>.com/rvaser/bioparser<span class="idiff right">/actions/workflows/bioparser.yml/badge.svg</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown">Bioparser is a c++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></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">@@ -38,8 +38,8 @@ If you are not using CMake, include the appropriate header file directly to your</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p">-</span> (optional) cmake 3.11+</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###### Hidden</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) biosoup 0.10.0</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) googletest 1.10.0</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) <span class="idiff left right">rvaser/</span>biosoup 0.10.0</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) <span class="idiff left right">google/</span>googletest 1.10.0</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Examples</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">libbioparser-dev (3.0.1<span class="idiff left">3</span>-1) <span class="idiff right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbioparser-dev (3.0.1<span class="idiff left">5</span>-1) <span class="idiff right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> TODO: wait for libbiosoup-dev to enter the archive</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 08 Mar 2021 17:10:31 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Build-Depends: libbiosoup-dev</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> TODO: wait for libbiosoup-dev to enter the archive</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 15 Oct 2021 08:08:59 +0200</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">libbioparser-dev (3.0.12-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,9 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> libgtest-dev (>> 1.8.0-10~)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libgtest-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libbiosoup-dev</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libbioparser-dev</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libbioparser-dev.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/rvaser/bioparser/</span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/rvaser/bioparser/releases .*/<span class="idiff left right">archive/</span>@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/rvaser/bioparser/releases .*/@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#9e1a62480721ea8da8e2bc6a6c3cf9d790767f2d"><strong>include/bioparser/fastq_parser.hpp</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">@@ -85,7 +85,7 @@ class FastqParser: public Parser<T> {</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">is_quality</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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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">quality_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">storage_ptr</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC87" 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;">is_quality</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">storage_ptr</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">quality_ptr</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">=</span>=</span> <span class="n" style="color: #333;">comment_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">data_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">storage_ptr</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">quality_ptr</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">></span>=</span> <span class="n" style="color: #333;">comment_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">data_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">is_quality</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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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">is_name</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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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">create_T</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/0f8747db179d1b7abcbce1957928320c52182ef7...1b77cbd3bcbe424c592d0765e7b9cdc64c0876f7#ba35fbe579108bcc7bd6117bebf894744989f40a"><strong>include/bioparser/parser.hpp</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">@@ -7,6 +7,7 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cctype></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdint></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></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">@@ -82,11 +83,15 @@ class Parser { // Parser factory</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">buffer_bytes_</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">buffer_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Store</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">strip</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Store</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size</span>_t</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">strip</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">buffer_ptr_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">buffer_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[bioparser::Parser::Store] error: buffer overflow"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">storage_ptr_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[bioparser::Parser::Store] error: storage overflow"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">storage_ptr_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">storage_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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