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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcalm">Debian Med / bcalm</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/f2de5dc7dc5f9a1ea4f9310b63ae68b1680b13b1">f2de5dc7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T21:21:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/ef0bb8011cfe7b98e7f962807e69682b2638e9fb">ef0bb801</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T21:21:17+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/bcalm/-/commit/090cbad9acb5ed0a83a9c40191236537d8169267">090cbad9</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T21:21:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.2'
Update to upstream version '2.2.2'
with Debian dir f0a0c31fa96367262765400f2e81b1d2706397c8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/b66cc11f4e0cb4587a2fc0cf00b81f5cc16592dc">b66cc11f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T21:21:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/cc66c61487335b1a2214bb5c556c25da9989aaff">cc66c614</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-05T21:33:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusting patches - small quirky bits
</pre>
</li>
</ul>
<h4>17 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#fd5da61396a8376845bee5cdf71aaf3c98a888ae">
<span class="new-file">
+
.circleci/config.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#1d03bbf095557f92ea6b6f914caa2d3bb64b1772">
bidirected-graphs-in-bcalm2/bidirected-graphs-in-bcalm2.md
</a>
</li>
<li class="file-stats">
<a href="#f47b80d156de6f6bb3af12b9e2357cee35b0065c">
<span class="new-file">
+
debian/bcalm.docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#4e7bef039d1be849bcdebf9c5fa57692726875ec">
debian/bcalm.install
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#4cb57ff20a59a27e6f7d43c6dbcd32bed9df7ccb">
debian/patches/modify_cmake.patch
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#373718cc9dbf52c4bc22a279a0659a24406b4082">
<span class="new-file">
+
scripts/split_unitigs.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#af6a1b037ce2d18e6764ee124aef1618e8716808">
scripts/unitigEvaluator.cpp
</a>
</li>
<li class="file-stats">
<a href="#3e56fd432a8b3fe7f0547bf09b0866f184141588">
src/bcalm_1.cpp
</a>
</li>
<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
</a>
</li>
<li class="file-stats">
<a href="#cda8852985673cf0bc554ea5ae9603cc84312090">
<span class="new-file">
+
test/simple_test.sh
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="fd5da61396a8376845bee5cdf71aaf3c98a888ae">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#fd5da61396a8376845bee5cdf71aaf3c98a888ae"><strong>.circleci/config.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></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;">build</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;">docker</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;">image</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">debian:stretch"</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;">steps</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="pi">-</span> <span class="s" style="color: #d14;">checkout</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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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Installing SUDO</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sudo</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">rm</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-rf</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">/var/lib/apt/lists/*'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Installing GCC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build-essential</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">wget</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">zlib1g</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">zlib1g-dev'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Installing Git</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">git'</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</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;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Getting submodules</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;">command</span><span class="pi">:</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="s" style="color: #d14;">git submodule init </span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="s" style="color: #d14;">git submodule update --remote</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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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;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install CMAKE</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;">command</span><span class="pi">:</span> <span class="pi">|</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">wget https://cmake.org/files/v3.10/cmake-3.10.2-Linux-x86_64.tar.gz</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">tar -xvzf cmake-3.10.2-Linux-x86_64.tar.gz</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;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ccmake</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;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cmake</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cpack</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;">chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ctest</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;">DIR=$(pwd)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ccmake /usr/bin/ccmake</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;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cmake /usr/bin/cmake</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cpack /usr/bin/cpack</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="s" style="color: #d14;">ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ctest /usr/bin/ctest</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</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;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install CPPUnit</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">update</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sudo</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">apt-get</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-y</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">libcppunit-dev'</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Compiling</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;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">mkdir</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cmake</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">..</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">make</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-j</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4'</span></span>
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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;">run</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Making package in case we'll release</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;">command</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">make</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">package</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">mkdir</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">../artifacts</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">mv</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">bcalm-binaries-*.tar.gz</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">../artifacts'</span></span>
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46
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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;">store_artifacts</span><span class="pi">:</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">./artifacts</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> </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;">publish-github-release</span><span class="pi">:</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;">docker</span><span class="pi">:</span></span>
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51
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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;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">cibuilds/github:0.10</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;">steps</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">attach_workspace</span><span class="pi">:</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">at</span><span class="pi">:</span> <span class="s" style="color: #d14;">./artifacts</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></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;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Publish</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Release</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">GitHub"</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">command</span><span class="pi">:</span> <span class="pi">|</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="s" style="color: #d14;">VERSION=$(cat VERSION)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="s" style="color: #d14;">ghr -t ${GITHUB_TOKEN} -u ${CIRCLE_PROJECT_USERNAME} -r ${CIRCLE_PROJECT_REPONAME} -c ${CIRCLE_SHA1} -delete ${VERSION} ./artifacts/</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"><span class="na" style="color: #008080;">workflows</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">main</span><span class="pi">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">filters</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span> <span class="s" style="color: #d14;">/^v?\d+\.\d+\.\d+$/</span></span>
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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;">publish-github-release</span><span class="pi">:</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">requires</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="pi">-</span> <span class="s" style="color: #d14;">build</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="na" style="color: #008080;">filters</span><span class="pi">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" 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="LC73" class="line" lang="yaml"> <span class="na" style="color: #008080;">ignore</span><span class="pi">:</span> <span class="s" style="color: #d14;">/.*/</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span> <span class="s" style="color: #d14;">/^v?\d+\.\d+\.\d+$/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -36,7 +36,7 @@ before_deploy:</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"><span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">releases</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">api_key</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">hQsQR/iRTVbDDJlyJpBln98CT+Mm9GHy/H/gYvLwhoh73f+OmUEreB2HS/KsWp3TTgZeI/ANRBpY11I4Xrai1sntqjXO2LG79pEIoL62AcCBEQJ1RsnkGg9s10qFKzQqImuPDzincnVIrSr92L8kcXBuErU2YK7/Ss5ABzxRN+E</span>=</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">KW6qAyrtX1fyCpZEjttW4YaKRGFvioqYBoN3mvlGJeYJqTFvuPbQ4PMA+ueQWvQFImhF74C/WQjnw0uUgRpBUV5mQZOFqA0QIGJNaIkL/dSqs7N9YI97VX3TH/GxPsLpW1KfQPF0DkCJ8pobWEz5k3Itl8woSXcX2HskxtQNKA0</span>=</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">file</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">${RELEASE_FILE}"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -17,16 +17,26 @@ FOREACH (path "${CMAKE_CURRENT_SOURCE_DIR}/cmake" "${GATB_CORE_HOME}/gatb-core/c</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDFOREACH</span><span class="p">(</span>path<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#############################</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>getting git version</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#getting git version</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#from http://stackoverflow.com/questions/1435953/how-can-i-pass-git-sha1-to-compiler-as-definition-using-cmake</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">exec_program</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"git"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cmake"> ARGS <span class="s2" style="color: #d14;">"rev-parse --short HEAD"</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cmake"> OUTPUT_VARIABLE VERSION_SHA1 <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"> OUTPUT_VARIABLE VERSION_SHA1</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"> RETURN_VALUE ERROR_GIT<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span> -DGIT_SHA1=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">VERSION_SHA1</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ERROR_GIT</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span> -DGIT_SHA1=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">VERSION_SHA1</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"Warning: cannot retrieve git version. Bcalm won't display its version. Error value: </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ERROR_GIT</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ERROR_GIT</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#add version nifo</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">file</span> <span class="p">(</span>STRINGS <span class="s2" style="color: #d14;">"VERSION"</span> VERSION<span class="p">)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span> -DVERSION=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">)</span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cmake"></span>
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31
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>
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32
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># THIRD PARTIES</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +115,7 @@ SET (CPACK_SOURCE_IGNORE_FILES</td>
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105
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># We copy the project binary to the 'bin' directory</span></span>
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106
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>TARGETS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> DESTINATION bin<span class="p">)</span></span>
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107
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>DIRECTORY <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/example/"</span> DESTINATION example<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>FILES LICENSE README.md DESTINATION bin/..<span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>FILES <span class="idiff left right">VERSION </span>LICENSE README.md DESTINATION bin/..<span class="p">)</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cmake"></span>
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110
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># cmake_system_name for mac is Darwin, i want to change that</span></span>
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111
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SYSTEM_NAME</span><span class="si" style="color: #d14;">}</span> MATCHES <span class="s2" style="color: #d14;">"Linux"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,9 +124,6 @@ elseif (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")</td>
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114
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PRETTY_SYSTEM_NAME <span class="s2" style="color: #d14;">"Mac"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">file</span> <span class="p">(</span>STRINGS <span class="s2" style="color: #d14;">"VERSION"</span> VERSION<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>CPACK_PACKAGE_FILE_NAME <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>-binaries-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="si" style="color: #d14;">}</span>-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PRETTY_SYSTEM_NAME</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span> <span class="p">(</span>CPack<span class="p">)</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,6 +39,10 @@ Download the latest [Linux/MacOS binaries](https://github.com/GATB/bcalm/release</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="sb" style="color: #d14;"> git clone --recursive https://github.com/GATB/bcalm </span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd bcalm</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mkdir build; cd build; cmake ..; make -j 8</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">You can also install bcalm from <span class="p">[</span><span class="nv" style="color: #008080;">bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bioconda.github.io/</span><span class="p">)</span> with <span class="p">[</span><span class="nv" style="color: #008080;">conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.conda.io/en/latest/</span><span class="p">)</span>:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install -c conda-forge -c bioconda bcalm</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"><span class="gh" style="color: #999;"># Input formats</span></span>
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<pre style="margin: 0;"> <span id="LC48" 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">@@ -97,6 +101,6 @@ BCALM 2 produces some intermediate files: a .h5 file (or a _gatb/ folder), which</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Acknowledgements</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown">If using BCALM 2, please cite:</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown">Rayan Chikhi, Antoine Limasset and Paul Medvedev, Compacting de Bruijn graphs from sequencing data quickly and in low memory, Proceedings of ISMB 2016, Bioinformatics, 32 (12): i201-i208. (<span class="p">[</span><span class="nv" style="color: #008080;">Bibtex</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">://bioinformatics.oxfordjournals.org/citmgr?type=bibtex&gca=bioinfo%3B32%2F12%2Fi201</span></span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">Rayan Chikhi, Antoine Limasset and Paul Medvedev, Compacting de Bruijn graphs from sequencing data quickly and in low memory, Proceedings of ISMB 2016, Bioinformatics, 32 (12): i201-i208. (<span class="p">[</span><span class="nv" style="color: #008080;">Bibtex</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s://academic.oup.com/Citation/Download?resourceId=2289008&resourceType=3&citationFormat=2</span></span><span class="p">)</span>)</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown">This project has been supported in part by NSF awards DBI-1356529, CCF-1439057, IIS-1453527, and IIS-1421908.</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">v2.2.<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">v2.2.<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#1d03bbf095557f92ea6b6f914caa2d3bb64b1772"><strong>bidirected-graphs-in-bcalm2/bidirected-graphs-in-bcalm2.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +25,7 @@ The table contains the 8 edge types, organized such that each row lists a pair o</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig3</span><span class="p">](</span><span class="sx" style="color: #d14;">fig33.png</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">Bi-directed graphs have the <span class="idiff left right">constraint</span> that, given two nodes x and y, a label l, and a mirror type, either both or none of the mirror edges with label l exist between x and y. Informally, edges always come in identically-labeled pairs (with one exception listed below). Thus, even though there are 8 type of edges that can be between x and y, there are really only 4 types of <span class="ge" style="font-style: italic;">*connections*</span>. There are alternate representations of bi-directed graphs that remove this redundancy, but we do not describe them here.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">Bi-directed graphs have the <span class="ge" style="font-style: italic;"><span class="idiff left right">*mirror constraint*</span></span> that, given two nodes x and y, a label l, and a mirror type, either both or none of the mirror edges with label l exist between x and y. Informally, edges always come in identically-labeled pairs (with one exception listed below). Thus, even though there are 8 type of edges that can be between x and y, there are really only 4 types of <span class="ge" style="font-style: italic;">*connections*</span>. There are alternate representations of bi-directed graphs that remove this redundancy, but we do not describe them here.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">The above rule has an interesting effect on self-loops (i.e. when e.from = e.to). In such cases, observe that the two mirror edges of Type 3 are identical. The same holds for Type 4. We refer to such edges as <span class="ge" style="font-style: italic;">*self-mirrors*</span>. A bi-directed graph does not allow to represent duplicate edges, and so this connection is represented by only one edge. This case forms an exception to the rule that all edges come in pairs with their mirror. I suspect that this special case has cost humanity thousand of hours in debugging time. </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">@@ -50,16 +50,16 @@ We label each edge with the length of the equal suffixes/prefixes. For example,</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig5</span><span class="p">](</span><span class="sx" style="color: #d14;">fig5.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown">Intuitively, an edge implies that the strings of the two nodes can be combined, using an overlap, into a bigger string. The sign at a node indicates whether the label or the label's reverse-complement is used. A '+' indicates that the label is used, while a '-' indicates that the label's reverse-complement is used. </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">Intuitively, an edge implies that the strings of the two nodes can be combined, using an overlap, into a bigger string. The sign at a node indicates whether the label or the label's reverse-complement is used. A '+' indicates that the label is used, while a '-' indicates that the label's reverse-complement is used. <span class="idiff left">This is called the </span><span class="ge" style="font-style: italic;"><span class="idiff">*spelling rule*</span></span><span class="idiff right">. In this case, for example, the string spelled by the top edge is AAGTCTAC.</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown">Notice that the two overlaps between the nodes in the previous example are mirror edges of type 4. This is not a coincidence. One can show from the properties of reverse-complements that if there is an overlap implied by an edge, then there must also be an overlap implied by the mirror of that edge. </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">Notice that the two overlaps between the nodes in the previous example are mirror edges of type 4. This is not a coincidence. One can show from the properties of reverse-complements that if there is an overlap implied by an edge, then there must also be an overlap implied by the mirror of that edge. <span class="idiff left right">Thus, our definition of edges in a bi-directed overlap graph satisfies the mirror constraint of bi-directed graphs.</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown">In this context, a self-mirror edge corresponds to a situation where either a suffix or a prefix of a node is equal to its own reverse-complement. Here is an example of a Type 3 self-mirror. Note that a self-mirror cannot have an overlap with an odd length, because an odd-length string can never be its own reverse-complement.</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig6</span><span class="p">](</span><span class="sx" style="color: #d14;">fig66.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Bidirected de-Bruijn graph</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Bi<span class="idiff left right">-</span>directed de-Bruijn graph</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown">Given a set of strings S, a <span class="ge" style="font-style: italic;">*[node-centric](https://www.biostars.org/p/175058/#256741) bi-directed de-Bruijn graph of order k*</span> is a type of bi-directed overlap graph. The nodes correspond to all the distinct k-mer substrings of S, with the caveat that two k-mers that are reverse-complements of each other are represented by a single node. The label of this node is chosen arbitrarily as either the k-mer or its reverse complement; however there is often a convention that the label is chosen as the lexicographically smallest option. The edges correspond to all the overlaps of length k-1. For example, with k = 3 and S={GTATAC}, the graph is:</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">@@ -68,25 +68,28 @@ Given a set of strings S, a *[node-centric](https://www.biostars.org/p/175058/#2</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown">Here, we gave each edge a name (e.g. e1) so that we can refer to the edges below. Observe that e1 and e2 are mirror edges, while e3 is a self-mirror and e4 is a self-mirror.</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Walks and unitigs and compaction</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Walks </span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown">A sequence of edges e<span class="nt" style="color: #000080;"><sub></span>1<span class="nt" style="color: #000080;"></sub></span>, ... , e<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span> in a bi-directed graph is <span class="ge" style="font-style: italic;">*walk*</span> if </span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="p">*</span> It is a walk in the directed sense, i.e. e<span class="nt" style="color: #000080;"><sub></span>i<span class="nt" style="color: #000080;"></sub></span>.to = e<span class="nt" style="color: #000080;"><sub></span>i+1<span class="nt" style="color: #000080;"></sub></span>.from, for all 0 < i < n.</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"><span class="p">*</span> The signs at an internal vertices are equal, i.e. e<span class="nt" style="color: #000080;"><sub></span>i<span class="nt" style="color: #000080;"></sub></span>.toSign = e<span class="nt" style="color: #000080;"><sub></span>i+1<span class="nt" style="color: #000080;"></sub></span>.fromSign, for all 0 < i < n.</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">A single vertex is also considered a walk. In the previous graph example, the sequence (e2, e3, e4, e3, e1) is a walk, while (e2, e3, e4, e1) is not.</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown">In a bi-directed overlap graph, a walk spells a corresponding string. For example, (e2, e3, e1) spells the original string GTATAC, while (e3, e1) spells TATAC. Observe that each walk has a corresponding <span class="ge" style="font-style: italic;">*mirror walk*</span> which spells the reverse-complement. For example, the mirror walk of (e3, e1) is (e2, e3) and spells GTATA.</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">In a bi-directed overlap graph, a walk spells a corresponding string using the spelling rule previously described. For example, (e2, e3, e1) spells the original string GTATAC, while (e3, e1) spells TATAC. Observe that each walk has a corresponding <span class="ge" style="font-style: italic;">*mirror walk*</span> which spells the reverse-complement. For example, the mirror walk of (e3, e1) is (e2, e3) and spells GTATA.</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Unitigs and compaction</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown">Given a walk (e<span class="nt" style="color: #000080;"><sub></span>1<span class="nt" style="color: #000080;"></sub></span>, ..., e<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span>), let v<span class="nt" style="color: #000080;"><sub></span>0<span class="nt" style="color: #000080;"></sub></span> = e<span class="nt" style="color: #000080;"><sub></span>1<span class="nt" style="color: #000080;"></sub></span>.from and v<span class="nt" style="color: #000080;"><sub></span>i<span class="nt" style="color: #000080;"></sub></span> = e<span class="nt" style="color: #000080;"><sub></span>i<span class="nt" style="color: #000080;"></sub></span>.to, for all 1 <= i <= n. A walk is a <span class="ge" style="font-style: italic;">*unitig*</span> if it is either a single vertex or a path (i.e. does not repeat vertices) such that</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="p">*</span> for every 0 <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="na" style="color: #008080;">n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">the</span> <span class="na" style="color: #008080;">only</span> <span class="na" style="color: #008080;">edges</span> <span class="na" style="color: #008080;">incident</span> <span class="na" style="color: #008080;">on</span> <span class="na" style="color: #008080;">v</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span><span class="na" style="color: #008080;">sub</span><span class="nt" style="color: #000080;">></span>i<span class="nt" style="color: #000080;"></sub></span> are e<span class="nt" style="color: #000080;"><sub></span>i-1<span class="nt" style="color: #000080;"></sub></span>, e<span class="nt" style="color: #000080;"><sub></span>i<span class="nt" style="color: #000080;"></sub></span>, and their mirrors.</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="p">*</span> e<span class="nt" style="color: #000080;"><sub></span>1<span class="nt" style="color: #000080;"></sub></span> is the only outgoing edge from v<span class="nt" style="color: #000080;"><sub></span>0<span class="nt" style="color: #000080;"></sub></span> that has the the sign e<span class="nt" style="color: #000080;"><sub></span>1<span class="nt" style="color: #000080;"></sub></span>.fromSign at v<span class="nt" style="color: #000080;"><sub></span>0<span class="nt" style="color: #000080;"></sub></span>,</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="p">*</span> e<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span> is the only incoming edge to v<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span> that has the sign e<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span>.toSign at v<span class="nt" style="color: #000080;"><sub></span>n<span class="nt" style="color: #000080;"></sub></span>.</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown">A unitig is <span class="ge" style="font-style: italic;">*maximal*</span> if it cannot be extended in either direction. Consider the graph defined by the rectangular nodes and solid edges below (i.e. discarding the rhombus-shaped nodes and dashed edges for now)<span class="idiff left right">, In this graph, there is a maximal unitig traversing (B, C, D, E). There is also a mirror maximal unitig traversing (E, D, C, B). There are also 4 other maximal unitigs: (A), (H), (K), and (I). The rhombus-shaped nodes and dashed edges represent nodes and edges that, if added to the graph, would destroy the unitig (B, C, D, E) and its mirror</span>.</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown">A unitig is <span class="ge" style="font-style: italic;">*maximal*</span> if it cannot be extended in either direction. Consider the graph defined by the rectangular nodes and solid edges below (i.e. discarding the rhombus-shaped nodes and dashed edges for now)<span class="idiff left right">. In this graph, there is a maximal unitig traversing (B, C, D, E). There is also a mirror maximal unitig traversing (E, D, C, B). There are also 4 other maximal unitigs: (A), (H), (K), and (I). The rhombus-shaped nodes and dashed edges represent nodes and edges that, if added to the graph, would destroy the unitig (B, C, D, E) and its mirror. The maximal unitigs of the graph would then be (K), (A), (B), (C), (D), (E), (I), and (H)</span>.</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig8</span><span class="p">](</span><span class="sx" style="color: #d14;">fig8.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown">In the <span class="ge" style="font-style: italic;">*compacted*</span> bi-directed graph, every maximal unitig and its mirror is replaced by a single vertex. Formally, the nodes of the compacted graph are the maximal unitigs, and the edges represent all overlaps of length k-1.</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown">In the <span class="ge" style="font-style: italic;">*compacted*</span> bi-directed graph, every maximal unitig and its mirror is replaced by a single vertex. Formally, the nodes of the compacted graph are the maximal unitigs<span class="idiff left right"> (grouped in mirror pairs)</span>, and the edges represent all overlaps of length k-1.</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">The unitig definition is motivated by the desire for it to have the following properties (though I have not seen a formal proof of these in the bi-directed setting):</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="p">*</span> Maximal unitigs should be a vertex decomposition of the graph; in particular, two maximal unitigs should not share a vertex</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">@@ -4,4 +4,3 @@ debian/missing-sources/simple_test.sh usr/share/doc/bcalm/test</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">example</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">compare_fasta</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span></pre>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bcalm</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcalm (2.2.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Don't install VERSION file to /usr</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 05 May 2020 21:21:17 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">bcalm (2.2.1-2) unstable; urgency=medium</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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#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">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> cmake</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bcalm</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bcalm.git</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/GATB/bcalm</span>
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<li id="4cb57ff20a59a27e6f7d43c6dbcd32bed9df7ccb">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#4cb57ff20a59a27e6f7d43c6dbcd32bed9df7ccb"><strong>debian/patches/modify_cmake.patch</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">@@ -6,9 +6,9 @@ Last-Update: 2019-09-23</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">Index: bcalm/CMakeLists.txt</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcalm.orig/CMakeLists.txt<span class="idiff left right"> 2019-09-23 06:21:21.709546638 +0100</span></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcalm/CMakeLists.txt<span class="idiff left right"> 2019-09-23 06:21:21.705546591 +0100</span></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -5,12 +5,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcalm.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcalm/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -5,12 +5,12 @@</span><span class="idiff left right"> cmake_minimum_required(VERSION 2.6)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> # Shortcuts</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> ################################################################################</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">@@ -23,29 +23,38 @@ Index: bcalm/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> IF (EXISTS "${path}")</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> SET (CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${path}")</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> ENDIF()</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -19,1<span class="idiff left right">3 +19,15 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -19,1<span class="idiff left">8 +19,18 @@</span></span><span class="idiff right"> ENDFOREACH(path)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> #############################</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> #<span class="idiff left right"> </span>getting git version</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #getting git version</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> #from http://stackoverflow.com/questions/1435953/how-can-i-pass-git-sha1-to-compiler-as-definition-using-cmake</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-exec_program(</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "git"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CMAKE_CURRENT_SOURCE_DIR}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARGS "rev-parse --short HEAD"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- OUTPUT_VARIABLE VERSION_SHA1 )</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- OUTPUT_VARIABLE VERSION_SHA1</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RETURN_VALUE ERROR_GIT)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if(NOT ${ERROR_GIT})</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- add_definitions( -DGIT_SHA1="${VERSION_SHA1}" )</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else()</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- message("Warning: cannot retrieve git version. Bcalm won't display its version. Error value: ${ERROR_GIT})")</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif(NOT ${ERROR_GIT})</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#exec_program(</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "git"</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# ${CMAKE_CURRENT_SOURCE_DIR}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# ARGS "rev-parse --short HEAD"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# OUTPUT_VARIABLE VERSION_SHA1 )</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# OUTPUT_VARIABLE VERSION_SHA1</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# RETURN_VALUE ERROR_GIT)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if(NOT ${ERROR_GIT})</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# add_definitions( -DGIT_SHA1="${VERSION_SHA1}" )</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# message("Warning: cannot retrieve git version. Bcalm won't display its version. Error value: ${ERROR_GIT})")</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif(NOT ${ERROR_GIT})</span></span>
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41
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_definitions( -DGIT_SHA1="${VERSION_SHA1}" )</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# NEEDS CHANGING PER UPSTREAM CHANGE</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_definitions( -DGIT_SHA1="ed86d2c")</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> ################################################################################</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="p">@@ -39,7 +41,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> ################################</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> #add version nifo</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -49,7 +49,10 @@</span> SET (GATB_CORE_EXCLUDE_EXAMPLES 1)</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> # GATB CORE</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">@@ -57,7 +66,7 @@ Index: bcalm/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> # TOOLS</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">70,7 +75,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">80,7 +83,7 @@</span></span><span class="idiff right"> set (PROGRAM_SOURCE_DIR ${PROJECT_SOURCE</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> include_directories (${PROGRAM_SOURCE_DIR})</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles ${PROGRAM_SOURCE_DIR}/*.cpp)</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> add_executable(${program} ${ProjectFiles})</span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -14,4 +14,5 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> rm -r debian/bcalm/usr/example \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> debian/bcalm/usr/README.md \</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> debian/bcalm/usr/LICENSE</span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> debian/bcalm/usr/LICENSE \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> debian/bcalm/usr/VERSION</span></pre>
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<li id="373718cc9dbf52c4bc22a279a0659a24406b4082">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#373718cc9dbf52c4bc22a279a0659a24406b4082"><strong>scripts/split_unitigs.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"split BCALM unitigs at reference extremities. More specifically:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" the script considers the sets B and E of all k-mers that are extremities of the reference genomes/contigs, respectively B for beginnings of contigs and E for ends."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" output is: modified unitigs such that each k-mer in B should be the beginning of an unitig, and each kmer in E should be end of an unitig."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" in order words, unitigs are split at kmers that are extremities of the reference sequences"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"This script is a small modification of pufferize.py"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"arguments: references.fa unitigs.fa k"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">references</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">unitigs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://www.biostars.org/p/710/#1412</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">groupby</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fasta_iter</span><span class="p">(</span><span class="n" style="color: #333;">fasta_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> given a fasta file. yield tuples of header, sequence</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ditch the boolean (x[0]) and just keep the header or sequence since</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we know they alternate.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">faiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">">"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">faiter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># drop the ">"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">:].</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># join all sequence lines to one.</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">faiter</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">complement</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span> <span class="s" style="color: #d14;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">:</span> <span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">:</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">:</span> <span class="s" style="color: #d14;">'A'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">reverse_complement</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">complement</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reverse_complement</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kmer</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#ref_kmers=set()</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parse references</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#for header, ref in fasta_iter(references):</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for kmer in [ref[:k], ref[-k:]]:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ref_kmers.add(normalize(kmer))</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print(kmer)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># go through all reference strings and keep the starting and end kmers for each of them in the ref_skmers and ref_ekmers respectively.</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">ref_skmers</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">ref_ekmers</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parse references</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_iter</span><span class="p">(</span><span class="n" style="color: #333;">references</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">ref_skmers</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">ref_ekmers</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parse unitigs and split if necessary</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ASSUMPTION: we might need to split a unitig multiple times</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># NOTE: the exact position of the split in unitig depends on whether the seen kmer is the first or last kmer in a reference string.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># NOTE: unitigs are renumbered consecutively</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># NOTE: unitigs links are discarded</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".split.fa"</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">nb_unitigs</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">save_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span><span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">nb_unitigs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">unitig%s</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">%s</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="n" style="color: #333;">unitig_skmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="n" style="color: #333;">unitig_ekmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">unitig_skmer</span><span class="p">,</span> <span class="n" style="color: #333;">unitig_ekmer</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">k</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">unitig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">unitig_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">save_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unitig_skmer</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning, start kmer (%s) was also seen at start of unitig %s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">],</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">unitig_skmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])])))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unitig_ekmer</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning, start kmer (%s) was also seen at end of unitig %s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">],</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">unitig_ekmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])])))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unitig_skmer</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning, last kmer (%s) was also seen at start of unitig %s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:],</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">unitig_skmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])])))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">unitig_ekmer</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning, last kmer (%s) was also seen at end of unitig %s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:],</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">unitig_ekmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])])))</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">unitig_ekmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="p">:])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">unitig_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)]</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">unitig_skmer</span><span class="p">[</span><span class="n" style="color: #333;">normalize</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">[:</span><span class="n" style="color: #333;">k</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">unitig_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)]</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Start parsing and spliting unitigs .. "</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_iter</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</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="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="p">]</span> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># cut up until first kmer but not the kmer itself</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kmer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_skmers</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_ekmers</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">k</span><span class="p">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">create_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="n" style="color: #333;">prev</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># cut the unitig until the kmer, including it</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kmer</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_ekmers</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_skmers</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">create_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="n" style="color: #333;">prev</span><span class="p">:</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="p">])</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#add the last and right most unitig:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">k</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">create_unitig</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span><span class="p">[</span><span class="n" style="color: #333;">prev</span><span class="p">:])</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"done. result is in: %s.split.fa"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">unitigs</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#af6a1b037ce2d18e6764ee124aef1618e8716808"><strong>scripts/unitigEvaluator.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// it can be compiled with just:</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// g++ -lomp -o unitigEvaluator unitigEvaluator.cpp</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// updated: 27th November 2018</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 6th june 2019</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// WARNING: reference needs to be one line per sequence</span></span>
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9
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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 <fstream></span></span>
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8
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10
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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 <cstring></span></span>
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11
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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 <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">@@ -11,15 +13,10 @@</td>
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13
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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 <iostream></span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <chrono></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_set></span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "sparsepp/spp.h"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_map></span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <omp.h></span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">xs</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">y</span><span class="p">){</span></span>
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24
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">^=</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">13</span><span class="p">);</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">^=</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">17</span><span class="p">);</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">^=</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">15</span><span class="p">));</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,13 +106,13 @@ int main(int argc, char ** argv){</td>
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109
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Problem with files opening"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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110
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">FP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">TP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">FN</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">size</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">number</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">genomicKmersNum</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">FP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">TP</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">FN</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">size</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">number</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">genomicKmersNum</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)<span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">genomicDuplicated</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">omp_lock_t</span> <span class="n" style="color: #333;">lock</span><span class="p">[</span><span class="mi" style="color: #099;">1024</span><span class="p">];</span></span>
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114
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">omp_init_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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116
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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117
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">HASH</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span><span class="n" style="color: #333;">HASH</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nbHash</span><span class="p">;</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">HASH</span><span class="p">){</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">s<span class="idiff left right">parse_hash</span>_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">genomicKmers</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">unordered</span>_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">genomicKmers</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">genomicKmers</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma omp parallel num_threads(nb_cores)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -179,6 +176,8 @@ int main(int argc, char ** argv){</td>
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179
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#pragma omp atomic</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">TP</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">genomicDuplicated</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="p">}</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">@@ -212,6 +211,8 @@ int main(int argc, char ** argv){</td>
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212
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"True positive (kmers in the unitig and the references) GOOD kmers: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">intToString</span><span class="p">(</span><span class="n" style="color: #333;">TP</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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213
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"False positive (kmers in the unitig and NOT in the references) ERRONEOUS kmers: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">intToString</span><span class="p">(</span><span class="n" style="color: #333;">FP</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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214
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"False Negative (kmers NOT in the unitig but in the references) MISSING kmers: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">intToString</span><span class="p">(</span><span class="n" style="color: #333;">FN</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genomicDuplicated</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"REPEATED kmers in the unitigs (should not happen): "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">intToString</span><span class="p">(</span><span class="n" style="color: #333;">genomicDuplicated</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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215
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Erroneous kmer rate (*10,000): "</span><span class="o" style="font-weight: 600;"><<</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">FP</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">FP</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">TP</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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216
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Missing kmer rate (*10,000): "</span><span class="o" style="font-weight: 600;"><<</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">FN</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">genomicKmersNum</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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217
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>
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<li id="3e56fd432a8b3fe7f0547bf09b0866f184141588">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#3e56fd432a8b3fe7f0547bf09b0866f184141588"><strong>src/bcalm_1.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,21 +61,34 @@ struct Functor { void operator () (bcalm_1 *bcalm)</td>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">OptionFailure</span> <span class="p">(</span><span class="n" style="color: #333;">bcalm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getParser</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Specifiy -in"</span><span class="p">);</span></span>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// delete the .h5 file</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">delete_h5_file</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">delete_h5_file</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copies the h5 naming mechanism in GraphUnitigs.cpp</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcalm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_INPUT</span><span class="p">);</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcalm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_OUTPUT</span><span class="p">))</span> </span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcalm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_OUTPUT</span><span class="p">);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">getBaseName</span> <span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">prefix</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".h5"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="p">};</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">bcalm_1</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">execute</span> <span class="p">(){</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef GIT_SHA1</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BCALM 2, git commit "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GIT_SHA1</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;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BCALM 2, <span class="idiff left">version "</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">VERSION</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">", </span>git commit "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GIT_SHA1</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;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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74
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** we get the kmer size chosen by the end user. */</span></span>
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75
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span> <span class="p">(</span><span class="n" style="color: #333;">STR_KMER_SIZE</span><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>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"due to a currently known bug, bcalm with a kmer multiple of 4 is temporarily unavailable. please retry with another k-mer size"</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;">endl</span><span class="p">;</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We launch Minia with the correct Integer implementation according to the choosen kmer size. */</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">apply</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Functor</span><span class="p">,</span><span class="n" style="color: #333;">bcalm_1</span><span class="o" style="font-weight: 600;">*></span> <span class="p">(</span><span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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81
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,9 +28,9 @@ int main (int argc, char* argv[])</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef GIT_SHA1</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">STR_VERSION</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"-v"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BCALM 2, git commit "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GIT_SHA1</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;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BCALM 2, <span class="idiff left">version "</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">VERSION</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">", </span>git commit "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GIT_SHA1</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;">endl</span><span class="p">;</span></span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Using gatb-core version "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">info</span><span class="p">().</span><span class="n" style="color: #333;">getVersion</span><span class="p">()</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;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_<span class="idiff left right">FAILURE</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_<span class="idiff left right">SUCCESS</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/63dd846f06a6d99653cc7ccab1b981acd3165d6f...cc66c61487335b1a2214bb5c556c25da9989aaff#cda8852985673cf0bc554ea5ae9603cc84312090"><strong>test/simple_test.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"> </span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> reference.fasta</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell">wget https://raw.githubusercontent.com/GATB/MindTheGap/f5cb0fec816686c7393772787d736565c4f056a4/test/full_test/reference.fasta <span class="o" style="font-weight: 600;">></span>& /dev/null</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">../build/bcalm <span class="nt" style="color: #000080;">-in</span> reference.fasta <span class="nt" style="color: #000080;">-abundance-min</span> 1 <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">></span>& /dev/null</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> reference.unitigs.fa.glue<span class="k" style="font-weight: 600;">*</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> compare_fasta.py</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">wget https://raw.githubusercontent.com/GATB/minia/master/test/compare_fasta.py <span class="o" style="font-weight: 600;">></span>& /dev/null</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">python compare_fasta.py reference.fasta reference.unitigs.fa</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">res</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$?</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> reference.fasta reference.h5 reference.unitigs.fa compare_fasta.py </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$res</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"0"</span> <span class="o" style="font-weight: 600;">]</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"test OK"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"test KO"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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