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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/racon">Debian Med / racon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a">f4e54d01</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-12-19T22:12:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.0</pre>
</li>
</ul>
<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#22a3274c95efed4a549ef01d54508637d6bf29e3">
<span class="new-file">
+
.github/workflows/racon.yml
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
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<li class="file-stats">
<a href="#cff5932439e9d9af5fa49ecf5e6d617527da6495">
scripts/racon_wrapper.py
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<li class="file-stats">
<a href="#a4f795e94afebe43cb4224bc334439bf472c5526">
src/cuda/cudapolisher.cpp
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<li class="file-stats">
<a href="#a5a7b76c67b308f1d3ac8995827cde0ee87db68e">
src/polisher.cpp
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<li class="file-stats">
<a href="#68894cb44c1c4108edb4a74b7f6747bf9cb92782">
test/meson.build
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<li class="file-stats">
<a href="#693654edd1082408d152bbeaa3b25a7424a0b8b5">
test/racon_test.cpp
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<li class="file-stats">
<a href="#01b178486728d401ff32ecb4ed339b4111075c64">
<span class="deleted-file">
−
test/racon_test_config.h.in
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<li class="file-stats">
<a href="#3f123297a2ab808cdd64559741aaae3f90f5e173">
vendor/meson.build
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<h4>Changes:</h4>
<li id="22a3274c95efed4a549ef01d54508637d6bf29e3">
<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#22a3274c95efed4a549ef01d54508637d6bf29e3"><strong>.github/workflows/racon.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">racon CI</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">BUILD_TYPE</span><span class="pi">:</span> <span class="s" style="color: #d14;">Release</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang++</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang++-4.0</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler == 'g++-4.8' }}</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup GCC</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">egor-tensin/setup-gcc@v1</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">4.8"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">platform</span><span class="pi">:</span> <span class="s" style="color: #d14;">x64</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler == 'clang++-4.0' }}</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup Clang</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">egor-tensin/setup-clang@v1</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">4.0"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">platform</span><span class="pi">:</span> <span class="s" style="color: #d14;">x64</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Configure CMake</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake -B ${{ github.workspace }}/build -DCMAKE_BUILD_TYPE=${{ env.BUILD_TYPE }}</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">CXX</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.compiler }}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">cmake --build ${{ github.workspace }}/build --config ${{ env.BUILD_TYPE }}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">working-directory</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ github.workspace }}/build</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="s" style="color: #d14;">bin/racon --version</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="s" style="color: #d14;">bin/racon_test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GCC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4.8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># GCC 4.8.5 & CMake 3.9.2</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.5</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 3.5.0 & CMake 3.9.2</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-trusty-3.5</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.5</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${SET_COMPILER}"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build && git checkout 703bd9c</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_CXX_FLAGS="-std=c++11" .. && make && sudo make install</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd ../../</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build && cd build</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -Dspoa_build_executable=ON -Dracon_build_tests=ON -Dracon_build_wrapper=ON -DCMAKE_BUILD_TYPE=Release .. && make</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./bin/racon --version</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./bin/racon_test</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.2<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>racon<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_version 1.4.21<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.11<span class="p">)</span></span>
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4
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff">CMAKE_ARCHIVE_OUTPUT_DIRECTORY </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">PROJECT_BINARY_DIR</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff">/lib</span><span class="p"><span class="idiff right">)</span></span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff">CMAKE_LIBRARY_OUTPUT_DIRECTORY </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">PROJECT_BINARY_DIR</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff">/lib</span><span class="p"><span class="idiff right">)</span></span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff">CMAKE_RUNTIME_OUTPUT_DIRECTORY </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">PROJECT_BINARY_DIR</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff right">/bin</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;"><span class="idiff left">project</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right">racon VERSION 1.5.0</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="idiff left right"> LANGUAGES CXX</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="idiff left"> DESCRIPTION </span><span class="s2" style="color: #d14;"><span class="idiff right">"Racon is a consensus module for de novo genome assembly."</span></span><span class="p">)</span></span>
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8
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
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9
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -Wall -Wextra -pedantic"</span><span class="p">)</span></span>
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10
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 11<span class="p">)</span></span>
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11
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<td class="new_line diff-line-num" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD_REQUIRED ON<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="12" 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">
12
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<td class="new_line diff-line-num" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_EXTENSIONS OFF<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13" 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">
13
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<td class="new_line diff-line-num" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_build_tests <span class="s2" style="color: #d14;">"Build racon unit tests"</span> OFF<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_build_wrapper <span class="s2" style="color: #d14;">"Build racon wrapper"</span> OFF<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_enable_cuda <span class="s2" style="color: #d14;">"Build racon with NVIDIA CUDA support"</span> OFF<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cmake"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Check CUDA compatibility.</span></span>
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19
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>CUDA 9.0 QUIET REQUIRED<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" 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">
21
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC21" 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;">CUDA_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>FATAL_ERROR <span class="s2" style="color: #d14;">"CUDA not detected on system. Please install"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="24" 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">
24
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">"Using CUDA </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> from </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_TOOLKIT_ROOT_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="25" 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">
25
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CUDA_NVCC_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_NVCC_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -lineinfo"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="26" 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">
26
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="28" 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">
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<td class="new_line diff-line-num new" 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="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_ARCHIVE_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/lib<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="28" 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">
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_LIBRARY_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/lib<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_RUNTIME_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="28" 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">
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>FetchContent<span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>GNUInstallDirs<span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR<span class="p">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_main_project ON<span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_build_tests <span class="s2" style="color: #d14;">"Build unit tests"</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_main_project</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_build_wrapper <span class="s2" style="color: #d14;">"Build wrapper"</span> OFF<span class="p">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>racon_enable_cuda <span class="s2" style="color: #d14;">"Build with NVIDIA CUDA support"</span> OFF<span class="p">)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>bioparser 3.0.15 QUIET<span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT bioparser_FOUND<span class="p">)</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"> bioparser</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/rvaser/bioparser</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"> GIT_TAG 3.0.15<span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>bioparser<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 class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT bioparser_POPULATED<span class="p">)</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>bioparser<span class="p">)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">bioparser_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">bioparser_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"> EXCLUDE_FROM_ALL<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 class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cmake"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>edlib 1.2.7 QUIET<span class="p">)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT edlib_FOUND<span class="p">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cmake"> edlib</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/martinsos/edlib</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cmake"> GIT_TAG v1.2.7<span class="p">)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cmake"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>edlib<span class="p">)</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT edlib_POPULATED<span class="p">)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>edlib<span class="p">)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">edlib_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">edlib_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>spoa 4.0.8 QUIET<span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT spoa_FOUND<span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"> spoa</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/rvaser/spoa</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cmake"> GIT_TAG 4.0.8<span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cmake"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>spoa<span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT spoa_POPULATED<span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>spoa<span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">spoa_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">spoa_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</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="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cmake"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>thread_pool 4.0.0 QUIET<span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT thread_pool_FOUND<span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cmake"> thread_pool</span>
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<td class="new_line diff-line-num new" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/rvaser/thread_pool</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cmake"> GIT_TAG 4.0.0<span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>thread_pool<span class="p">)</span></span>
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<td class="new_line diff-line-num new" 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="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT thread_pool_POPULATED<span class="p">)</span></span>
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<td class="new_line diff-line-num new" 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="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>thread_pool<span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">thread_pool_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">thread_pool_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</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="cmake"><span class="nb" style="color: #0086b3;">endif</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="cmake"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_build_tests<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>GTest 1.10.0 QUIET<span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT GTest_FOUND<span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</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="cmake"> googletest</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/google/googletest</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cmake"> GIT_TAG release-1.10.0<span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>googletest<span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT googletest_POPULATED<span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>googletest<span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">googletest_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">googletest_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>GTest::Main ALIAS gtest_main<span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</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="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cmake"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_build_wrapper<span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>rampler 2.0.0 QUIET<span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT rampler_FOUND<span class="p">)</span></span>
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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;">FetchContent_Declare</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="cmake"> rampler</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/rvaser/rampler</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cmake"> GIT_TAG 2.0.0<span class="p">)</span></span>
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28
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cmake"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</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>/src<span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>rampler<span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT rampler_POPULATED<span class="p">)</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>rampler<span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">rampler_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">rampler_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cmake"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>CUDA 9.0 QUIET REQUIRED<span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>FATAL_ERROR <span class="s2" style="color: #d14;">"CUDA not detected on system. Please install"</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span> <span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">"Using CUDA </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> from </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_TOOLKIT_ROOT_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CUDA_NVCC_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CUDA_NVCC_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -lineinfo"</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>DEFINED CLARAGENOMICSANALYSIS_SDK_PATH<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND CMAKE_PREFIX_PATH <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SDK_PATH</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/cmake"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>cudapoa REQUIRED<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>cudaaligner REQUIRED<span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">elseif</span> <span class="p">(</span>DEFINED CLARAGENOMICSANALYSIS_SRC_PATH<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudapoa<span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SRC_PATH</span><span class="si" style="color: #d14;">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudaaligner<span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SRC_PATH</span><span class="si" style="color: #d14;">}</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span> <span class="p">()</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cmake"> genomeworks</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/clara-parabricks/GenomeWorks</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cmake"> GIT_TAG v0.5.3<span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cmake"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>genomeworks<span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT genomeworks_POPULATED<span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>genomeworks<span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">genomeworks_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">genomeworks_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" 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="LC172" 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="LC173" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_sources</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cmake"> src/main.cpp</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cmake"> src/logger.cpp</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cmake"> src/polisher.cpp</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cmake"> src/overlap.cpp</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cmake"> src/sequence.cpp</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cmake"> src/window.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND racon_sources src/cuda/cudapolisher.cpp src/cuda/cudabatch.cpp src/cuda/cudaaligner.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">cuda_add_executable</span><span class="p">(</span>racon <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon PRIVATE CUDA_ENABLED<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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="LC44" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>racon <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cmake"> src/logger.cpp</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cmake"> src/polisher.cpp</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cmake"> src/overlap.cpp</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cmake"> src/sequence.cpp</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cmake"> src/window.cpp<span class="p">)</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Add version information to bibary.</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon PRIVATE RACON_VERSION=<span class="s2" style="color: #d14;">"v</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_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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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/src<span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND racon_sources</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cmake"> src/cuda/cudapolisher.cpp</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cmake"> src/cuda/cudabatch.cpp</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cmake"> src/cuda/cudaaligner.cpp<span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cmake"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">cuda_add_library</span><span class="p">(</span>racon</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cmake"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cmake"> PRIVATE CUDA_ENABLED<span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span> <span class="p">()</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>racon</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cmake"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cmake"> bioparser::bioparser</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cmake"> edlib::edlib</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cmake"> spoa::spoa</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cmake"> thread_pool::thread_pool<span class="p">)</span></span>
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49
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cmake"></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET bioparser<span class="p">)</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/spoa/vendor/bioparser EXCLUDE_FROM_ALL<span class="p">)</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET spoa<span class="p">)</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/spoa EXCLUDE_FROM_ALL<span class="p">)</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET thread_pool<span class="p">)</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/thread_pool EXCLUDE_FROM_ALL<span class="p">)</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET edlib<span class="p">)</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/edlib EXCLUDE_FROM_ALL<span class="p">)</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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62
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>DEFINED CLARAGENOMICSANALYSIS_SDK_PATH<span class="p">)</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND CMAKE_PREFIX_PATH <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SDK_PATH</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/cmake"</span><span class="p">)</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>cudapoa REQUIRED<span class="p">)</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>cudaaligner REQUIRED<span class="p">)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">elseif</span> <span class="p">(</span>DEFINED CLARAGENOMICSANALYSIS_SRC_PATH<span class="p">)</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudapoa<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SRC_PATH</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="70" 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">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudaaligner<span class="p">)</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CLARAGENOMICSANALYSIS_SRC_PATH</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" 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">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" 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">
74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">elseif</span><span class="p">(</span>EXISTS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/vendor/GenomeWorks<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudapoa<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/GenomeWorks <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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78
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<td class="new_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudaaligner<span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/GenomeWorks <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudapoa<span class="p">)</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>../GenomeWorks <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" 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="LC85" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET cudaaligner<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>../GenomeWorks <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/GenomeWorks EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" 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="LC88" 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="LC89" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cmake"> cudapoa</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cmake"> cudaaligner<span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cmake"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_include_directories</span><span class="p">(</span>racon PUBLIC</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/src><span class="p">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cmake"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>racon_exe</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cmake"> src/main.cpp<span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cmake"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon_exe</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cmake"> racon<span class="p">)</span></span>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon bioparser spoa thread_pool edlib_static<span class="p">)</span></span>
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92
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon cudapoa cudaaligner<span class="p">)</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" 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="LC220" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon_exe</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cmake"> PRIVATE CUDA_ENABLED<span class="p">)</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" 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="LC223" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon_exe PRIVATE VERSION=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>TARGET racon_exe PROPERTY OUTPUT_NAME racon<span class="p">)</span></span>
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95
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cmake"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS racon DESTINATION <span class="idiff left right">bin</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS racon<span class="idiff left">_exe</span> DESTINATION <span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">CMAKE_INSTALL_BINDIR</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span><span class="p">)</span></span>
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97
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cmake"></span>
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98
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_build_tests<span class="p">)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>GTest REQUIRED<span class="p">)</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_test_data_path <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/test/data/<span class="p">)</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">configure_file</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/test/racon_test_config.h.in"</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/config/racon_test_config.h"</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/config<span class="p">)</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</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>/src<span class="p">)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cmake"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_test_sources</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cmake"> test/racon_test.cpp</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cmake"> src/logger.cpp</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cmake"> src/polisher.cpp</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cmake"> src/overlap.cpp</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cmake"> src/sequence.cpp</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cmake"> src/window.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span>APPEND racon_test_sources src/cuda/cudapolisher.cpp src/cuda/cudabatch.cpp src/cuda/cudaaligner.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">cuda_add_executable</span><span class="p">(</span>racon_test <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_test_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon_test PRIVATE CUDA_ENABLED<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC118" 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="LC119" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>racon_test <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">racon_test_sources</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC120" 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="LC121" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon_test bioparser spoa thread_pool edlib_static GTest::Main<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon_test cudapoa cudaaligner<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="LC230" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>racon_test</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cmake"> test/racon_test.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>racon_test</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cmake"> racon</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cmake"> GTest::Main<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon_test</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cmake"> PRIVATE TEST_DATA=<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;">/test/data/"</span><span class="p">)</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cmake"></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>racon_test</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cmake"> PRIVATE CUDA_ENABLED<span class="p">)</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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126
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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127
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cmake"></span>
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128
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_build_wrapper<span class="p">)</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_path <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin/racon<span class="p">)</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>rampler_path <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/vendor/rampler/bin/rampler<span class="p">)</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">configure_file</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/scripts/racon_wrapper.py</span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_FILES_DIRECTORY</span><span class="si" style="color: #d14;">}</span>/racon_wrapper<span class="p">)</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">file</span><span class="p">(</span>COPY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_FILES_DIRECTORY</span><span class="si" style="color: #d14;">}</span>/racon_wrapper</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cmake"> FILE_PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cmake"> WORLD_READ WORLD_EXECUTE<span class="p">)</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cmake"></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET rampler<span class="p">)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/rampler<span class="p">)</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_path <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin/racon<span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>rampler_path <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/_deps/rampler-build/bin/rampler<span class="p">)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>racon_enable_cuda<span class="p">)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_wrapper_enable_cuda True<span class="p">)</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" 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="LC252" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_wrapper_enable_cuda False<span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">configure_file</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/scripts/racon_wrapper.py</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_FILES_DIRECTORY</span><span class="si" style="color: #d14;">}</span>/racon_wrapper<span class="p">)</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">file</span><span class="p">(</span>COPY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_FILES_DIRECTORY</span><span class="si" style="color: #d14;">}</span>/racon_wrapper</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cmake"> FILE_PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cmake"> WORLD_READ WORLD_EXECUTE<span class="p">)</span></span>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cmake"></span>
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143
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Add Debian packaging</span></span>
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144
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_GENERATOR <span class="s2" style="color: #d14;">"DEB"</span><span class="p">)</span></span>
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145
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_DEBIAN_PACKAGE_MAINTAINER <span class="s2" style="color: #d14;">"Robert Vaser"</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">racon_version</span></span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;"><span class="idiff left right">PROJECT_VERSION</span></span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CPack<span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all clean meson cmake debug dist<span class="idiff left right"> modules</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all clean meson cmake debug dist</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">meson</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</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="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> build build-meson</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nl">meson</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">modules</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">VENDOR_FILES</span><span class="o" style="font-weight: 600;">=</span>vendor/thread_pool/README.md vendor/spoa/README.md vendor/rampler/README.md vendor/GenomeWorks/README.md</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nl">meson</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${VENDOR_FILES}</span></span>
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9
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<td class="new_line diff-line-num" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[Invoking Meson]"</span></span>
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10
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> build-meson <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>build-meson <span class="o" style="font-weight: 600;">&&</span> meson <span class="nt" style="color: #000080;">--buildtype</span><span class="o" style="font-weight: 600;">=</span>release <span class="nt" style="color: #000080;">-Dc_args</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Dtests</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">&&</span> ninja</span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nl">rebuild</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">modules</span></span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nl">rebuild</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">${VENDOR_FILES}</span></span></span>
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13
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<td class="new_line diff-line-num" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[Running Ninja only]"</span></span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"> <span class="p">@</span>ninja <span class="nt" style="color: #000080;">-C</span> build-meson</span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"><span class="nl">cmake</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">modules</span></span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="nl">cmake</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">${VENDOR_FILES}</span></span></span>
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17
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<td class="new_line diff-line-num" data-linenumber="19" 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">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[Invoking CMake]"</span></span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> build <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>build <span class="o" style="font-weight: 600;">&&</span> cmake <span class="nt" style="color: #000080;">-DCMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>Release <span class="nt" style="color: #000080;">-Dracon_build_tests</span><span class="o" style="font-weight: 600;">=</span>ON .. <span class="o" style="font-weight: 600;">&&</span> make</span>
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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">modules</span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">${VENDOR_FILES}</span></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[Invoking Meson]"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> build-debug <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>build-debug <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span>meson <span class="nt" style="color: #000080;">--buildtype</span><span class="o" style="font-weight: 600;">=</span>debugoptimized <span class="nt" style="color: #000080;">-Db_sanitize</span><span class="o" style="font-weight: 600;">=</span>address <span class="nt" style="color: #000080;">-Dtests</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> ninja</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nl">dist</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">release</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>build <span class="o" style="font-weight: 600;">&&</span> ninja-dist</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"><span class="nl"><span class="idiff left right">modules</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="nl"><span class="idiff left right">vendor/%/README.md</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[Fetching submodules]"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"> <span class="p">@</span>git submodule update <span class="nt" style="color: #000080;">--init</span></span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#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">@@ -9,7 +9,7 @@ Consensus module for raw de novo DNA assembly of long uncorrected reads.</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Description</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">Racon can be used as a polishing tool after the assembly with <span class="gs" style="font-weight: 600;"><span class="idiff left">**</span>either <span class="idiff right">Illumina</span> data or data produced by third generation of sequencing**</span>. The type of data inputed is automatically detected.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Racon can be used as a polishing tool after the assembly with either <span class="gs" style="font-weight: 600;"><span class="idiff left">**short accurate</span> data<span class="idiff">**</span></span> or <span class="gs" style="font-weight: 600;"><span class="idiff">**</span>data produced by third generation of sequencing**</span>. The type of data input<span class="idiff">t</span>ed is automatically detected.<span class="idiff right"> Although, Racon expects single-end short reads, while paired-end reads should be renamed with unique names up to the first whitespace and joined into a single file before mapping (which can be done with misc/racon_preprocess.py).</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files <span class="gs" style="font-weight: 600;">**can be compressed with gzip**</span> (which will have impact on parsing time).</span>
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<pre style="margin: 0;"> <span id="LC15" 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">@@ -31,22 +31,14 @@ A **wrapper script** is also available to enable easier usage to the end-user fo</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">To install Racon run the following commands:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">git clone <span class="nt" style="color: #000080;">--recursive</span> https://github.com/lbcb-sci/racon.git racon</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>racon</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir </span>build</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>build</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">cmake <span class="nt" style="color: #000080;">-DCMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>Release ..</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">git clone https://github.com/lbcb-sci/racon <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>racon <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">mkdir </span>build <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>build</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">cmake <span class="nt" style="color: #000080;">-DCMAKE_BUILD_TYPE</span><span class="o" style="font-weight: 600;">=</span>Release .. <span class="o" style="font-weight: 600;">&&</span> make</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown">After successful installation, an executable named <span class="sb" style="color: #d14;">`racon`</span> will appear in <span class="sb" style="color: #d14;">`build/bin`</span>.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">After successful installation, an executable named <span class="sb" style="color: #d14;">`racon`</span> will appear in <span class="sb" style="color: #d14;">`build/bin`</span><span class="idiff left"> (alongside unit tests </span><span class="sb" style="color: #d14;"><span class="idiff">`racon_test`</span></span><span class="idiff right">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown">Optionally, you can run <span class="sb" style="color: #d14;">`sudo make install`</span> to install racon executable to your machine.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">***Note**</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>: if you omitted <span class="sb" style="color: #d14;">`--recursive`</span> from <span class="sb" style="color: #d14;">`git clone`</span>, run <span class="sb" style="color: #d14;">`git submodule update --init --recursive`</span> before proceeding with compilation.</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown">To build unit tests add <span class="sb" style="color: #d14;">`-Dracon_build_tests=ON`</span> while running <span class="sb" style="color: #d14;">`cmake`</span> (Gtest required). After installation, an executable named <span class="sb" style="color: #d14;">`racon_test`</span> will be created in <span class="sb" style="color: #d14;">`build/bin`</span>.</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown">To build the wrapper script add <span class="sb" style="color: #d14;">`-Dracon_build_wrapper=ON`</span> while running <span class="sb" style="color: #d14;">`cmake`</span>. After installation, an executable named <span class="sb" style="color: #d14;">`racon_wrapper`</span> (python script) will be created in <span class="sb" style="color: #d14;">`build/bin`</span>.</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### CUDA Support</span></span>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project(</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> 'Racon',</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> 'cpp',</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> version : '1.<span class="idiff left right">4.13</span>',</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> version : '1.<span class="idiff left right">5.0</span>',</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> default_options : [</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> 'buildtype=release',</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 'warning_level=3',</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> 'cpp_std=c++11'],</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> license : 'MIT',</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> meson_version : '>= 0.<span class="idiff left right">48</span>')</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> meson_version : '>= 0.<span class="idiff left right">50.0</span>')</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">cpp = meson.get_compiler('cpp')</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,6 +19,7 @@ opt_compile_with_tests = get_option('tests')</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">racon_warning_flags = []</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">racon_cpp_flags = []</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">racon_macros = ['-DVERSION="' + meson.project_version() + '"']</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">################</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># Dependencies #</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" 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="102" 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">@@ -101,7 +102,7 @@ racon_dep = declare_dependency(</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> link_with: [racon_lib, vendor_lib],</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> dependencies: [racon_thread_dep, racon_zlib_dep],</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> version: meson.project_version(),</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> compile_args: racon_warning_flags + racon_cpp_flags)</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> compile_args: racon_warning_flags + racon_cpp_flags<span class="idiff left right"> + racon_macros</span>)</span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">if not meson.is_subproject()</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> racon_bin = executable(</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">@@ -111,12 +112,13 @@ if not meson.is_subproject()</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> dependencies : [racon_thread_dep, racon_zlib_dep],</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> include_directories : vendor_include_directories + racon_include_directories,</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> link_with : [racon_lib],</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> cpp_args : [racon_warning_flags, racon_cpp_flags])</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> cpp_args : [racon_warning_flags, racon_cpp_flags<span class="idiff left right">, racon_macros</span>])</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> ######################</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> # Tests #</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> ######################</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> if opt_compile_with_tests</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> racon_test_macros = ['-DTEST_DATA="' + meson.source_root() + '/test/data/"']</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> if gtest_dep.found()</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"> tests_bin = executable(</span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"> 'racon_test',</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">@@ -124,7 +126,7 @@ if not meson.is_subproject()</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> dependencies : [racon_thread_dep, racon_zlib_dep, gtest_dep],</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> include_directories : racon_include_directories + vendor_include_directories + racon_test_include_directories,</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> link_with : [racon_lib, vendor_lib],</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"> cpp_args : [racon_warning_flags, racon_cpp_flags, racon_test_extra_flags])</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> cpp_args : [racon_warning_flags, racon_cpp_flags, <span class="idiff left">racon_macros, </span>racon_test_extra_flags<span class="idiff right">, racon_test_macros</span>])</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> endif</span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> endif</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></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">@@ -15,7 +15,7 @@ class RaconWrapper:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="n" style="color: #333;">target_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">split</span><span class="p">,</span> <span class="n" style="color: #333;">subsample</span><span class="p">,</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">include_unpolished</span><span class="p">,</span> <span class="n" style="color: #333;">fragment_correction</span><span class="p">,</span> <span class="n" style="color: #333;">window_length</span><span class="p">,</span> <span class="n" style="color: #333;">quality_threshold</span><span class="p">,</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">error_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">error_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cudaaligner_band_width</span></span><span class="p"><span class="idiff right">,</span></span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">cudaaligner_batches</span><span class="p">,</span> <span class="n" style="color: #333;">cudapoa_batches</span><span class="p">,</span> <span class="n" style="color: #333;">cuda_banded_alignment</span><span class="p">):</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">sequences</span><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">@@ -35,9 +35,10 @@ class RaconWrapper:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatch</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gap</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.cudaaligner_batches = cudaaligner_batches</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.cudapoa_batches = cudapoa_batches</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.cuda_banded_alignment = cuda_banded_alignment</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_band_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cudaaligner_band_width</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_batches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cudaaligner_batches</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudapoa_batches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cudapoa_batches</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cuda_banded_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cuda_banded_alignment</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">work_directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/racon_work_directory_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,17 +120,20 @@ class RaconWrapper:</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">racon_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">RaconWrapper</span><span class="p">.</span><span class="n" style="color: #333;">__racon</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">include_unpolished</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'-u'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fragment_correction</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if (self.cuda_banded_alignment == True): racon_params.append('-b')</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'-w'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">window_length</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">quality_threshold</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'-e'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">error_threshold</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'-x'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gap</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># '--cudaaligner-batches', str(self.cudaaligner_batches),</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># '-c', str(self.cudapoa_batches),</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subsampled_sequences</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)])</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">racon_wrapper_enable_cuda</span><span class="o" style="font-weight: 600;">@</span><span class="p">):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cuda_banded_alignment</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'-b'</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">'--cudaaligner-band-width'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_band_width</span><span class="p">),</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">'--cudaaligner-batches'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_batches</span><span class="p">),</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cudapoa_batches</span><span class="p">)])</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">racon_params</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">subsampled_sequences</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">])</span></span>
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133
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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134
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">target_sequences_part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">split_target_sequences</span><span class="p">:</span></span>
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135
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">eprint</span><span class="p">(</span><span class="s" style="color: #d14;">'[RaconWrapper::run] processing data with racon'</span><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">@@ -187,10 +191,18 @@ if __name__ == '__main__':</td>
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187
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> mismatching bases'''</span><span class="p">)</span></span>
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188
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--gap'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''gap penalty (must be</span></span>
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189
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> negative)'''</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--threads'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of threads'''</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--cudaaligner-batches'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of batches for CUDA accelerated alignment'''</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cudapoa-batches'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of batches for CUDA accelerated polishing'''</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cuda-banded-alignment'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''use banding approximation for polishing on GPU. Only applicable when -c is used.'''</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--threads'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> threads'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--cudaaligner-band-width'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''Band</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> width for cuda alignment. Must be >= 0. Non-zero allows user defined</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> band width, whereas 0 implies auto band width determination.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--cudaaligner-batches'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> batches for CUDA accelerated alignment'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cudapoa-batches'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''number of</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> batches for CUDA accelerated polishing'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cuda-banded-alignment'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''use banding approximation for polishing on GPU. Only applicable</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> when -c is used.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" 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="210" 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">@@ -198,7 +210,8 @@ if __name__ == '__main__':</td>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">include_unpolished</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fragment_correction</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">window_length</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quality_threshold</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">error_threshold</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gap</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_batches</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cudapoa_batches</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cuda_banded_alignment</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_band_width</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cudaaligner_batches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cudapoa_batches</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cuda_banded_alignment</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">racon</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">racon</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#a4f795e94afebe43cb4224bc334439bf472c5526"><strong>src/cuda/cudapolisher.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">@@ -360,7 +360,7 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_failed_windows</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Submit</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">](</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_<span class="idiff left right">ids</span></span><span class="p">().</span><span class="n" style="color: #333;">find</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;">this_thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_id</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_<span class="idiff left right">map</span></span><span class="p">().</span><span class="n" style="color: #333;">find</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;">this_thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_id</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">window_consensus_status_</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">windows_</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">generate_consensus</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment_engines_</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">],</span> <span class="n" style="color: #333;">trim_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="p">},</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#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">@@ -12,11 +12,6 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "cuda/cudapolisher.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef RACON_VERSION</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#error "Undefined version for Racon. Please pass version using -DRACON_VERSION macro."</span></span>
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<pre style="margin: 0;">-<span id="LC17" 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="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RACON_VERSION</span><span class="p">;</span></span>
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20
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">CUDAALIGNER_INPUT_CODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">CUDAALIGNER_BAND_WIDTH_INPUT_CODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10001</span><span class="p">;</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></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="100" 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 +100,7 @@ int main(int argc, char** argv) {</td>
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105
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">num_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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106
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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107
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</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="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">version</span></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="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">VERSION</span></span><span class="p">);</span></span>
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109
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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110
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span></span>
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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;">help</span><span class="p">();</span></span>
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<li id="a5a7b76c67b308f1d3ac8995827cde0ee87db68e">
<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#a5a7b76c67b308f1d3ac8995827cde0ee87db68e"><strong>src/polisher.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" 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">@@ -30,7 +30,7 @@ namespace racon {</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">kChunkSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// ~ 1GB</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64_t</span></span> <span class="n" style="color: #333;">shrinkToFit</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;">vector</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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">>>&</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">begin</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></span> <span class="n" style="color: #333;">shrinkToFit</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;">vector</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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">>>&</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">begin</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" 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;">uint64_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</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;">src</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <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">@@ -49,11 +49,9 @@ uint64_t shrinkToFit(std::vector<std::unique_ptr<T>>& src, uint64_t begin) {</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">num_deletions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">src</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">src</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">num_deletions</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" 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;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Polisher</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">createPolisher</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequences_path</span><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">@@ -311,7 +309,7 @@ void Polisher::initialize() {</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">oparser_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">c</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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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">c</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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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">overlaps_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oparser_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="n" style="color: #333;">kChunkSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlaps_chunk</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -322,7 +320,7 @@ void Polisher::initialize() {</td>
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<pre style="margin: 0;"> <span id="LC320" 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;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;">overlaps_chunk</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span></span>
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<pre style="margin: 0;"> <span id="LC321" 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;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;">overlaps_chunk</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()));</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">c</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff right">l</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">l</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff right">c</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC324" 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;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</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;">overlaps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">transmute</span><span class="p">(</span><span class="n" style="color: #333;">sequences_</span><span class="p">,</span> <span class="n" style="color: #333;">name_to_id</span><span class="p">,</span> <span class="n" style="color: #333;">id_to_id</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"></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">@@ -340,11 +338,17 @@ void Polisher::initialize() {</td>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shrinkToFit</span><span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">n</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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<pre style="margin: 0;">+<span id="LC342" 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;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</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;">c</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">shrinkToFit</span><span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">remove_invalid_overlaps</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">l</span></span><span class="p">,</span> <span class="n" style="color: #333;">overlaps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">shrinkToFit</span><span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">l</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">remove_invalid_overlaps</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">c</span></span><span class="p">,</span> <span class="n" style="color: #333;">overlaps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">shrinkToFit</span><span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">c</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">overlaps</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,7 +496,7 @@ void Polisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,</td>
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496
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<pre style="margin: 0;"> <span id="LC496" 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;">uint64_t</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="n" style="color: #333;">windows_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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493
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_futures</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Submit</span><span class="p">(</span></span>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">](</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="p">{</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_<span class="idiff left right">ids</span></span><span class="p">().</span><span class="n" style="color: #333;">find</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;">this_thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_id</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thread_pool_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_<span class="idiff left right">map</span></span><span class="p">().</span><span class="n" style="color: #333;">find</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;">this_thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_id</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">windows_</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">generate_consensus</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment_engines_</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">],</span> <span class="n" style="color: #333;">trim_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="p">},</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#68894cb44c1c4108edb4a74b7f6747bf9cb92782"><strong>test/meson.build</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">@@ -8,7 +8,3 @@ racon_test_extra_flags = []</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">racon_test_config_h_vars = configuration_data()</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">racon_test_config_h_vars.set('racon_test_data_path', meson.source_root() + '/test/data/')</span></pre>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">racon_test_config_h = configure_file(</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> input : files('racon_test_config.h.in'),</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> output : 'racon_test_config.h',</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> configuration : racon_test_config_h_vars)</span></pre>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/f4e54d018bd2d041b9f99f3985febbc610e6810a#693654edd1082408d152bbeaa3b25a7424a0b8b5"><strong>test/racon_test.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">@@ -4,8 +4,6 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @brief Racon unit test source file</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "racon_test_config.h"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "sequence.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "polisher.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></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">@@ -71,23 +69,23 @@ TEST(RaconInitializeTest, SequencesPathExtensionError) {</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">RaconInitializeTest</span><span class="p">,</span> <span class="n" style="color: #333;">OverlapsPathExtensionError</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_DEATH</span><span class="p">((</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">createPolisher</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_DEATH</span><span class="p">((</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">createPolisher</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</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="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="LC74" class="line" lang="cpp"> <span class="s" style="color: #d14;">".racon::createPolisher. error: file has unsupported format extension "</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="s" style="color: #d14;">".valid extensions: .mhap, .mhap.gz, .paf, .paf.gz, .sam, .sam.gz.!"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="n" style="color: #333;">TEST</span><span class="p">(</span><span class="n" style="color: #333;">RaconInitializeTest</span><span class="p">,</span> <span class="n" style="color: #333;">TargetPathExtensionError</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">EXPECT_DEATH</span><span class="p">((</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">createPolisher</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_DEATH</span><span class="p">((</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">createPolisher</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span></span>
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83
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)),</span> <span class="s" style="color: #d14;">".racon::createPolisher. error: file has "</span></span>
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84
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="s" style="color: #d14;">"unsupported format extension .valid extensions: .fasta, .fasta.gz, .fna, "</span></span>
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85
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<td class="new_line diff-line-num" data-linenumber="83" 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">
83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="s" style="color: #d14;">".fna.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz.!"</span><span class="p">);</span></span>
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86
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualities</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</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="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="cpp"></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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="97" 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">@@ -99,7 +97,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualities) {</td>
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99
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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100
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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101
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</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="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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103
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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104
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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105
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></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="107" 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">@@ -109,8 +107,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualities) {</td>
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109
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="p">}</span></span>
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110
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"></span>
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111
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithoutQualities</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</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;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" 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="120" 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">@@ -122,7 +120,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualities) {</td>
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122
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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123
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"></span>
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124
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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126
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" 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="131" 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">@@ -133,8 +131,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualities) {</td>
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133
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="p">}</span></span>
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134
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesAndAlignments</span><span class="p">)</span> <span class="p">{</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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139
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"></span>
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140
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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="144" 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">@@ -146,7 +144,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignments) {</td>
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146
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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147
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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148
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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150
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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151
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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152
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="156" 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="154" 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">@@ -156,8 +154,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignments) {</td>
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156
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="p">}</span></span>
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157
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"></span>
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158
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithoutQualitiesAndWithAlignments</span><span class="p">)</span> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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162
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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163
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="167" 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">@@ -169,7 +167,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignments) {</td>
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169
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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170
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>
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171
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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173
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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174
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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175
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></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="177" 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">@@ -179,8 +177,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignments) {</td>
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179
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="p">}</span></span>
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180
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"></span>
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181
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesLargerWindow</span><span class="p">)</span> <span class="p">{</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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184
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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185
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"></span>
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186
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" 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="190" 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">@@ -192,7 +190,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindow) {</td>
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192
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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193
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"></span>
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194
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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196
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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197
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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198
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" 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="200" 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">@@ -202,8 +200,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindow) {</td>
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202
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="p">}</span></span>
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203
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"></span>
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204
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesEditDistance</span><span class="p">)</span> <span class="p">{</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</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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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"></span>
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209
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="215" 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="213" 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">@@ -215,7 +213,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistance) {</td>
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215
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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;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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216
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"></span>
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217
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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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;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC219" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="223" 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">@@ -225,8 +223,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistance) {</td>
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225
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualities</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</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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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><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">@@ -243,8 +241,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualities) {</td>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFull</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</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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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" 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="259" 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">@@ -261,8 +259,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFull) {</td>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithoutQualitiesFull</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</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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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>
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268
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" 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="277" 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">@@ -279,8 +277,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFull) {</td>
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279
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"><span class="p">}</span></span>
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280
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFullMhap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.mhap.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.mhap.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</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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285
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"></span>
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286
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" 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="296" 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">@@ -298,8 +296,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullMhap) {</td>
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298
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef CUDA_ENABLED</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="LC302" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="311" 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="309" 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">@@ -311,7 +309,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC315" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" 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="319" 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">@@ -321,8 +319,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithoutQualitiesCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="LC325" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="334" 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="332" 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">@@ -334,7 +332,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC338" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" 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="342" 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">@@ -344,8 +342,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesCUDA) {</td>
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344
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesAndAlignmentsCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="LC348" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" 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="355" 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">@@ -357,7 +355,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignmentsCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC361" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="367" 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="365" 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">@@ -367,8 +365,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesAndAlignmentsCUDA) {</td>
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367
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithoutQualitiesAndWithAlignmentsCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.sam.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="LC371" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="380" 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="378" 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">@@ -380,7 +378,7 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignmentsCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"></span>
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382
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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386
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" 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="388" 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">@@ -390,8 +388,8 @@ TEST_F(RaconPolishingTest, ConsensusWithoutQualitiesAndWithAlignmentsCUDA) {</td>
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390
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesLargerWindowCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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 class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</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="LC394" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" 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="401" 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">@@ -403,7 +401,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindowCUDA) {</td>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"></span>
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="413" 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="411" 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">@@ -413,8 +411,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesLargerWindowCUDA) {</td>
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413
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">ConsensusWithQualitiesEditDistanceCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_layout.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC417" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="426" 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="424" 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">@@ -426,7 +424,7 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistanceCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">polished_sequences</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="n" style="color: #333;">create_reverse_complement</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Create</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reference.fasta.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC430" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="436" 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="434" 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">@@ -436,8 +434,8 @@ TEST_F(RaconPolishingTest, ConsensusWithQualitiesEditDistanceCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kC</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC440" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><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">@@ -454,8 +452,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFullCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC458" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><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">@@ -472,8 +470,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesFullCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithoutQualitiesFullCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.paf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fasta.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC476" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><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">@@ -490,8 +488,8 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithoutQualitiesFullCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFullMhapCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.mhap.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">racon_test_data_path</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">SetUp</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sample_ava_overlaps.mhap.gz"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TEST_DATA</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"sample_reads.fastq.gz"</span><span class="p">,</span></span>
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PolisherType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">kF</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="LC494" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/*!</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> * @file racon_test_config.h.in</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> *</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * @brief Racon test configuration file</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> */</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#include <string></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">const std::string racon_test_data_path = "@racon_test_data_path@";</span></pre>
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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">@@ -4,9 +4,9 @@ vendor_cpp_sources = files([</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> 'rampler/src/sampler.cpp',</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> 'spoa/src/alignment_engine.cpp',</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> 'spoa/src/dispatcher.cpp',</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 'spoa/src/graph.cpp',</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> 'spoa/src/simd_alignment_engine_dispatch.cpp',</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> 'spoa/src/simd_alignment_engine_dispatcher.cpp',</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> 'spoa/src/sisd_alignment_engine.cpp',</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"></span>
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