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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/rampler">Debian Med / rampler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af">6976c32e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-19T07:36:42+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.0</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<li class="file-stats">
<a href="#0cbedd94e198319970f3660c670edb37b0d95f25">
src/sampler.cpp
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<li class="file-stats">
<a href="#2cd5061c4a1435b3df4eaa647d4dac4e157ae489">
src/sampler.hpp
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<a href="#33989c7ff155a4fed2047c4702a802ca716cb582">
<span class="deleted-file">
−
src/sequence.cpp
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<a href="#a62fd960b6b8c160d72e606a91e4a97b02f07bcf">
<span class="deleted-file">
−
src/sequence.hpp
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,41 +2,46 @@ dist: trusty</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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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;">compiler</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang</span></span>
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
</pre>
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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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<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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<td class="diff-line-num new new_line" data-linenumber="7" 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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<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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<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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<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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<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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<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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<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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<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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19
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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;">4.0</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 4.0 & CMake 3.9.2</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-trusty-4.0</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-4.0</span></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="s" style="color: #d14;">cmake</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;">env</span><span class="pi">:</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=clang-4.0 && export CXX=clang++-4.0"</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Xcode</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">9.0</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(OSX)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 9.0.0 & CMake 3.9.2</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;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode9</span></span>
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8
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"></span>
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9
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</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="c1" style="color: #998; font-style: italic;"># cmake 3.2</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo add-apt-repository ppa:george-edison55/cmake-3.x -y</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># g++4.8.1</span></span>
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14
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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;">if [ "$CXX" == "g++" ]; then sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; fi</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># clang 3.4</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" == "clang++" ]; then sudo add-apt-repository -y ppa:h-rayflood/llvm; fi</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"></span>
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19
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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;">sudo apt-get update -qq</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${SET_COMPILER}"</span></span>
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20
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"></span>
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21
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># cmake 3.2</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install cmake cmake-data</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># g++4.8.1</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" == "g++" ]; then sudo apt-get install -qq g++-4.8; fi</span></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="s" style="color: #d14;">if [ "$CXX" == "g++" ]; then export CXX="g++-4.8"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># clang 3.4</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" == "clang++" ]; then sudo apt-get install --allow-unauthenticated -qq clang-3.4; fi</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" == "clang++" ]; then export CXX="clang++-3.4"; fi</span></span>
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39
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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;">mkdir build && cd build</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release .. && make</span></span>
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32
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"></span>
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33
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></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="s" style="color: #d14;">mkdir build</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd build</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release ..</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</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/rampler --version</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="LC40" 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="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_success</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span></pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span></pre>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#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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2
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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>rampler<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 3.9<span class="p">)</span></span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" 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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5
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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_LIBRARY_OUTPUT_DIRECTORY </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">PROJECT_BINARY_DIR</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff">/lib</span><span class="p"><span class="idiff right">)</span></span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff">CMAKE_RUNTIME_OUTPUT_DIRECTORY </span><span class="si" style="color: #d14;"><span class="idiff">${</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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3
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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">rampler VERSION 2.0.0</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">"Rampler is a tool for subsampling or splitting FASTA/Q files."</span></span><span class="p">)</span></span>
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7
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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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8
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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;">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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9
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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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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10
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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>
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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>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>rampler</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cmake"> src/main.cpp</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cmake"> src/sequence.cpp</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cmake"> src/sampler.cpp<span class="p">)</span></span>
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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>
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13
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<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;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/lib<span class="p">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_RUNTIME_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin<span class="p">)</span></span>
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16
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span>
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17
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<pre style="margin: 0;"> <span id="LC16" 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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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/bioparser EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</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="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/bioparser EXCLUDE_FROM_ALL<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 class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
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>NOT TARGET biosoup<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;">add_subdirectory</span><span class="p">(</span>vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL<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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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>rampler bioparser<span class="p">)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"> src/main.cpp</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"> src/sampler.cpp<span class="p">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"> bioparser</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"> biosoup<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> PRIVATE</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"> RAMPLER_VERSION=<span class="s2" style="color: #d14;">"v</span><span class="si" style="color: #d14;">${</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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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS rampler DESTINATION bin<span class="p">)</span></span></pre>
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32
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<pre style="margin: 0;">+<span id="LC32" 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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_BINDIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Rampler</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Latest GitHub release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/rvaser/rampler.svg</span><span class="p">)</span>](https://github.com/rvaser/rampler/releases/latest)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status for c++/clang++</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">org/rvaser/rampler.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org</span>/rvaser/rampler)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status for c++/clang++</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">com/rvaser/rampler.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.com</span>/rvaser/rampler)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="idiff left right">Standalone module for sampling genomic sequences. It supports two modes, random subsampling of sequencer</span> data to a desired depth (given the reference length) and file splitting to desired size in bytes.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="idiff left right">Rampler is a standalone module for sampling genomic sequences. It supports two modes, random subsampling of sequencing</span> data to a desired depth (given the reference length) and file splitting to desired size in bytes.</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">Rampler takes as first input argument a file in FASTA/FASTQ format which can be compressed with gzip. The rest of input parameters depend on the mode of operation. The output is stored into a file(s) which is in the same format as the input file but uncompressed.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p">1.</span> gcc 4.8+ or clang 3.4+</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="p">2.</span> cmake 3.2+</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"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">To install Rampler run the following commands:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">To build rampler run the following commands:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">git clone <span class="nt" style="color: #000080;">--recursive</span> https://github.com/rvaser/rampler.git rampler</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>rampler</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir </span>build</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>build</span>
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<pre style="margin: 0;">-<span id="LC22" 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="LC23" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>rampler <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="LC14" 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="LC15" class="line" lang="markdown">./bin/rampler</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">After successful installation, an executable named <span class="sb" style="color: #d14;">`rampler`</span> will appear in <span class="sb" style="color: #d14;">`build/bin`</span>.</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">Optionally, you can run <span class="sb" style="color: #d14;">`sudo make install`</span> to install rampler executable to your machine.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><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="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">Usage of rampler is as following:</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> usage: rampler [options ...] <mode></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">which will display the following usage:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <mode></span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;"> subsample <sequences> <reference length> <coverage> [<coverage> ...]</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"><span class="sb" style="color: #d14;"> <sequences></span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;"> input file in FASTA/FASTQ format (can be compressed with gzip)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="sb" style="color: #d14;"> containing sequences to be subsampled</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <reference length></span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> integer denoting length of the reference genome (or</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"> assembly) from which the sequences originate</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <coverage></span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;"> integer denoting desired coverage of the subsampled</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sequences</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="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;"> split <sequences> <chunk size></span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <sequences></span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;"> input file in FASTA/FASTQ format (can be compressed with gzip)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;"> containing sequences which will be split into smaller chunks</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <chunk size></span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="sb" style="color: #d14;"> integer denoting the desired chunk size in bytes</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="sb" style="color: #d14;"> options:</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o, --out-directory</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"><span class="sb" style="color: #d14;"> default: current directory</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="sb" style="color: #d14;"> path in which sampled files will be created</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --version</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="sb" style="color: #d14;"> prints the version number</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -h, --help</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;"> prints out the help</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contact information</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">usage: rampler <span class="o" style="font-weight: 600;">[</span>options ...] <mode></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"> <mode></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"> subsample <sequences> <reference length> <coverage> <span class="o" style="font-weight: 600;">[</span><coverage> ...]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"> <sequences></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"> input file <span class="k" style="font-weight: 600;">in </span>FASTA/FASTQ format <span class="o" style="font-weight: 600;">(</span>can be compressed with <span class="nb" style="color: #0086b3;">gzip</span><span class="o" style="font-weight: 600;">)</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"> <reference length></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"> integer denoting length of the reference genome <span class="o" style="font-weight: 600;">(</span>or assembly<span class="o" style="font-weight: 600;">)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"> <coverage></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"> integer denoting desired coverage of the subsampled sequences</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"> <span class="nb" style="color: #0086b3;">split</span> <sequences> <chunk size></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"> <sequences></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"> input file <span class="k" style="font-weight: 600;">in </span>FASTA/FASTQ format <span class="o" style="font-weight: 600;">(</span>can be compressed with <span class="nb" style="color: #0086b3;">gzip</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"> containing sequences which will be <span class="nb" style="color: #0086b3;">split </span>into smaller chunks</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"> <chunk size></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"> integer denoting the desired chunk size <span class="k" style="font-weight: 600;">in </span>bytes</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"> options:</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-o</span>, <span class="nt" style="color: #000080;">--out-directory</span> <string></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"> default: current directory</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"> path <span class="k" style="font-weight: 600;">in </span>which sampled files will be created</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"> <span class="nt" style="color: #000080;">--version</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"> prints the version number</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-h</span>, <span class="nt" style="color: #000080;">--help</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"> prints out the <span class="nb" style="color: #0086b3;">help</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">```</span></span>
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68
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown">For additional information, help and bug reports please send an email to one of the following: robert.vaser@fer.hr</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">1.</span> gcc 4.8+ or clang 4.0+</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">2.</span> cmake 3.9+</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">3.</span> zlib</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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71
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Acknowledgment</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"></span>
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73
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown">This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353.</span></pre>
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<li id="b958235ee8db37bcaceda04b6d55553b450c2db4">
<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"><span class="idiff left right">#include <stdio.h></span></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"><span class="idiff left right">#include <stdlib.h></span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// Copyright (c) 2021 Robert Vaser</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></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 "bioparser/fasta_parser.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 "bioparser/fastq_parser.hpp"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "sampler.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"></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;"><span class="idiff left right">#include "bioparser/bioparser.hpp"</span></span></span>
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<pre style="margin: 0;">+<span id="LC12" 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">atomic</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></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="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">biosoup</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Sequence</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">num_objects</span></span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">};</span></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC10" 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="s" style="color: #d14;">"v1.1.1"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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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;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rampler_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RAMPLER_VERSION</span><span class="p">;</span></span>
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11
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">option</span> <span class="n" style="color: #333;">options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"out-directory"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"version"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"help"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</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"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></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="LC19" class="line" lang="cpp"> <span class="p"><span class="idiff left">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"out-directory"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">required_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">nullptr</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="p"><span class="idiff left">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"version"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">nullptr</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="p"><span class="idiff left">{</span></span><span class="s" style="color: #d14;"><span class="idiff">"help"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_argument</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">nullptr</span></span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="p"><span class="idiff left">{</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">nullptr</span></span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>
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17
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</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;">argv</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC23" 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;">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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">input_parameters</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC25" 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;">string</span> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">argument</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">argument</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"o:h"</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">argument</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">:</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="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;">version</span><span class="p">);</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" 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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<pre style="margin: 0;">-<span id="LC36" 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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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC38" 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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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;">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;">biosoup</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;">CreateParser</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <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;">path</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;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name</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;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ext</span><span class="p">)</span> <span class="p">{</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">is_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</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;">s</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;">suff</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</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;">suff</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="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">:</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">s</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;">suff</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suff</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suff</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="p">};</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="sc" style="color: #d14;">'/'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">c</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="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC35" 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;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">,</span> <span class="n" style="color: #333;">c</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="n" style="color: #333;">c</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="LC37" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">c</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa.gz"</span><span class="p">))</span> <span class="p">{</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</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="cpp"> <span class="k" style="font-weight: 600;">return</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;">biosoup</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 class="n" style="color: #333;">path</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</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;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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42
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="p">}</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::] error: too few arguments!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">help</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fastq"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fq"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fastq.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fq.gz"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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;">biosoup</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;">FastqParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</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;">invalid_argument</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">exception</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">exception</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">nullptr</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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC50" 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;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optind</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;">argc</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="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">input_parameters</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">argv</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="LC52" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">do_subsample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">do_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"subsample"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">do_subsample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"split"</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">do_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::] error: unkown mode %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;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::CreateParser] error: file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">path</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" has unsupported format extension (valid extensions: .fasta, "</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">".fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">nullptr</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="cpp"><span class="p">}</span></span>
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63
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">do_subsample</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">input_parameters</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="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">do_split</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">input_parameters</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="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Help</span><span class="p">()</span> <span class="p">{</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="s" style="color: #d14;">"usage: rampler [options ...] <mode></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <mode></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="s" style="color: #d14;">" subsample <sequences> <reference length> <coverage> [<coverage> ...]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <sequences></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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;">" input file in FASTA/FASTQ format (can be compressed with gzip)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <reference length></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting length of the reference genome (or assembly)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <coverage></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting desired coverage of the subsampled sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="s" style="color: #d14;">" split <sequences> <chunk size></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <sequences></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="s" style="color: #d14;">" input file in FASTA/FASTQ format (can be compressed with gzip)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <chunk size></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting the desired chunk size in bytes</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="s" style="color: #d14;">" options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -o, --out-directory <string></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="s" style="color: #d14;">" default: current directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="s" style="color: #d14;">" path in which sampled files will be created</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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;">" --version</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="s" style="color: #d14;">" prints the version number</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -h, --help</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="s" style="color: #d14;">" prints the usage</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="p">}</span></span>
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66
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::] error: missing input parameter(s)!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace</span></span>
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70
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">auto</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sampler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rampler</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">createSampler</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input_parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]);</span></span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sampler</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">initialize</span></span><span class="p"><span class="idiff right">()</span>;</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">do_split</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sampler</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">out_directory</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">atoi</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input_parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()))</span>;</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">do_subsample</span></span><span class="p">)</span> <span class="p">{</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">atoi</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input_parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">());</span></span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</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">3</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input_parameters</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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79
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<td class="diff-line-num new_line old" data-linenumber="98" 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="LC79" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sampler</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">subsample</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">out_directory</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_length</span></span><span class="p"><span class="idiff right">,</span></span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">atoi</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input_parameters</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()))</span>;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">main</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">argc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" 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">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></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="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">input_parameters</span></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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">arg</span></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">while</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">arg</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">getopt_long</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">argc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"o:h"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">switch</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">arg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">case</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'o'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">out_directory</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">optarg</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">break</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">case</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'v'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </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">cerr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rampler_version</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">endl</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">case</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'h'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Help</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="nl"><span class="idiff left">default:</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">;</span></span></span>
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82
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <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="p">}</span></span>
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83
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</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 class="n" style="color: #333;">Help</span><span class="p">();</span></span>
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84
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="p">}</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">optind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::] error: missing arguments!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optind</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;">argc</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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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">input_parameters</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <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>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">subsample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"subsample"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">subsample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"split"</span><span class="p">)</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="cpp"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::] error: unknown mode!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</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="p">}</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">subsample</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">input_parameters</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="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" 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="cpp"> <span class="p">(</span><span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">input_parameters</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="mi" style="color: #099;">3</span><span class="p">))</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="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::] error: missing arguments!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="p">}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" 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;">string</span> <span class="n" style="color: #333;">name</span><span class="p">{},</span> <span class="n" style="color: #333;">ext</span><span class="p">{};</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sparser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CreateParser</span><span class="p">(</span><span class="n" style="color: #333;">input_parameters</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="n" style="color: #333;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ext</span><span class="p">);</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sparser</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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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</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="cpp"> <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>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">rampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sampler</span> <span class="n" style="color: #333;">sampler</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">sparser</span><span class="p">),</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext</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;">sampler</span><span class="p">.</span><span class="n" style="color: #333;">Initialize</span><span class="p">();</span></span>
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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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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">)</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">sampler</span><span class="p">.</span><span class="n" style="color: #333;">Split</span><span class="p">(</span><span class="n" style="color: #333;">out_directory</span><span class="p">,</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">c_str</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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subsample</span><span class="p">)</span> <span class="p">{</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">reference_length</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;">input_parameters</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</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;">input_parameters</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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">sampler</span><span class="p">.</span><span class="n" style="color: #333;">Subsample</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;">out_directory</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="cpp"> <span class="n" style="color: #333;">reference_length</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;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">input_parameters</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="p">}</span></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</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="s" style="color: #d14;">"usage: rampler [options ...] <mode></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <mode></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="s" style="color: #d14;">" subsample <sequences> <reference length> <coverage> [<coverage> ...]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <sequences></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="s" style="color: #d14;">" input file in FASTA/FASTQ format (can be compressed with gzip)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="s" style="color: #d14;">" containing sequences to be subsampled</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <reference length></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting length of the reference genome (or</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="s" style="color: #d14;">" assembly) from which the sequences originate</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <coverage></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting desired coverage of the subsampled</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="s" style="color: #d14;">" sequences</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="s" style="color: #d14;">" split <sequences> <chunk size></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <sequences></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="s" style="color: #d14;">" input file in FASTA/FASTQ format (can be compressed with gzip)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="s" style="color: #d14;">" containing sequences which will be split into smaller chunks</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="s" style="color: #d14;">" <chunk size></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="s" style="color: #d14;">" integer denoting the desired chunk size in bytes</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="s" style="color: #d14;">" options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -o, --out-directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="s" style="color: #d14;">" default: current directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"> <span class="s" style="color: #d14;">" path in which sampled files will be created</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="s" style="color: #d14;">" --version</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"> <span class="s" style="color: #d14;">" prints the version number</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="s" style="color: #d14;">" -h, --help</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="s" style="color: #d14;">" prints the usage</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#0cbedd94e198319970f3660c670edb37b0d95f25"><strong>src/sampler.cpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file sampler.cpp</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @brief Sampler class 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="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright (c) 2021 Robert Vaser</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" 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 <random></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="LC9" 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="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "sampler.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/bioparser.hpp"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></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 <random></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 <stdexcept></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">rampler</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC16" 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="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC18" 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;">Sampler</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">createSampler</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 class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC20" 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;">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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sparser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span 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="n" style="color: #333;">base_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences_path</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="sc" style="color: #d14;">'/'</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="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">base_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base_name</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">base_name</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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;">string</span> <span class="n" style="color: #333;">extension</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">is_suffix</span> <span class="o" style="font-weight: 600;">=</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;">src</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;">suffix</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="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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;">suffix</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="LC28" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">src</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</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;">suffix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suffix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suffix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fasta.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fa.gz"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser</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;">createParser</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="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_path</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="cpp"> <span class="n" style="color: #333;">extension</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".fasta"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fastq"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fq"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fastq.gz"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_suffix</span><span class="p">(</span><span class="n" style="color: #333;">sequences_path</span><span class="p">,</span> <span class="s" style="color: #d14;">".fq.gz"</span><span class="p">))</span> <span class="p">{</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser</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;">createParser</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;">FastqParser</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_path</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="cpp"> <span class="n" style="color: #333;">extension</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".fastq"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::createSampler] error: "</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="s" style="color: #d14;">"file %s has unsupported format extension (valid extensions: "</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="s" style="color: #d14;">".fasta, .fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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;">Sampler</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Sampler</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">sparser</span><span class="p">),</span> <span class="n" style="color: #333;">base_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">extension</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC13" 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="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"><span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sampler</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;">unique_ptr</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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sparser</span><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;">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;">base_name</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;">extension</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sparser_</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">sparser</span><span class="p">)),</span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">base_name_</span><span class="p">(</span><span class="n" style="color: #333;">base_name</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">extension_</span><span class="p">(</span><span class="n" style="color: #333;">extension</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sampler</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="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;">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;">biosoup</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;">sparser</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="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;">base_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <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;">extension</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sparser_</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">sparser</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_length_</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">base_name_</span><span class="p">(</span><span class="n" style="color: #333;">base_name</span><span class="p">),</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">extension_</span><span class="p">(</span><span class="n" style="color: #333;">extension</span><span class="p">)</span> <span class="p">{</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="p">}</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"><span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">Sampler</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Initialize</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequences_length_</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initialize</span><span class="p">()</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="cpp"></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequences_length_</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::Sampler::initialize] warning: "</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="s" style="color: #d14;">"object already initialized!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser_</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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31
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<pre style="margin: 0;">+<span id="LC31" 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="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="mi" style="color: #099;">1ULL</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequences</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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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">}</span></span>
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71
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser_</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="LC73" 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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74
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<pre style="margin: 0;">-<span id="LC74" 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;">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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sequences</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</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;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">kChunkSize</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="cpp"></span>
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<pre style="margin: 0;">-<span id="LC77" 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;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_length_</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;">data</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="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <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;">status</span><span class="p">)</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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC37" 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;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_length_</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;">data</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="LC39" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="p">}</span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">subsample</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;">out_directory</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">reference_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">coverage</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">reference_length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">)</span> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::Sampler::subsample] warning: "</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="s" style="color: #d14;">"insufficient data for coverage %u!</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;">coverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Subsample</span><span class="p">(</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <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;">out_directory</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">reference_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">coverage</span><span class="p">)</span> <span class="p">{</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">reference_length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::Sampler::subsample] warning: "</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"insufficient data for coverage of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">coverage</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" 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;">random_device</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" 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;">mt19937</span> <span class="n" style="color: #333;">generator</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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;">uniform_real_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">reference_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">sequences_length_</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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;">string</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base_name_</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" 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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"x"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension_</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="cpp"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" 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;">ofstream</span> <span class="n" style="color: #333;">ofs</span><span class="p">(</span><span class="n" style="color: #333;">out_path</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="cpp"> <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;">ofs</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[rampler::Sampler::subsample] error: unable to create file on disk!"</span><span class="p">);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="p">}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser_</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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71
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<pre style="margin: 0;">+<span id="LC71" 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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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="mi" style="color: #099;">1ULL</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">30</span><span class="p">);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequences</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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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="p">}</span></span>
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95
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC96" 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;">random_device</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mt19937</span> <span class="n" style="color: #333;">generator</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC98" 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;">uniform_real_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">reference_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">sequences_length_</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>
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<pre style="margin: 0;">-<span id="LC103" 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;">string</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base_name_</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC104" 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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"x"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"w"</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out</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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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"rampler::Sampler::subsample] error: "</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="s" style="color: #d14;">"unable to create file %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;">out_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser_</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="LC113" 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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114
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<pre style="margin: 0;">-<span id="LC114" 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;">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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sequences</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</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;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">kChunkSize</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">-<span id="LC117" 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;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ratio</span><span class="p">)</span> <span class="p">{</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" 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;">quality</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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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</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;">%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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</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;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">c_str</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;">quality</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="p">}</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <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;">status</span><span class="p">)</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="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" 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;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ratio</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" 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;">quality</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="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <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;">data</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <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;">data</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <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;">quality</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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131
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="p">}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <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 class="p">}</span></span>
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133
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fclose</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">out</span></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="cpp"> <span class="n" style="color: #333;"><span class="idiff left">ofs</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">close</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">}</span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">split</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;">out_directory</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chunk_size</span><span class="p">)</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="cpp"></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chunk_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[rampler::Sampler::split] warning: "</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="s" style="color: #d14;">"insufficient data for chunk size %u!</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;">chunk_size</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Split</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;">out_directory</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chunk_size</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chunk_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">)</span> <span class="p">{</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[rampler::Sampler::split] warning: "</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"insufficient data for chunk size "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chunk_size</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <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>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chunk_number</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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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">sparser_</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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106
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<pre style="margin: 0;">+<span id="LC106" 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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</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;">chunk_size</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequences</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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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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143
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="p">}</span></span>
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144
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chunk_number</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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112
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<pre style="margin: 0;">+<span id="LC112" 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;">string</span> <span class="n" style="color: #333;">out_path</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="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base_name_</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">chunk_number</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension_</span><span class="p">;</span></span>
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146
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></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;">sparser_</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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148
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<pre style="margin: 0;">-<span id="LC148" 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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149
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<pre style="margin: 0;">-<span id="LC149" 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;">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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sequences</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparser_</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;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">chunk_size</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="cpp"></span>
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152
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<pre style="margin: 0;">-<span id="LC152" 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;">string</span> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_directory</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base_name_</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" 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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">chunk_number</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension_</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out</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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<td class="diff-line-num old old_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"rampler::Sampler::subsample] error: "</span></span>
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<td class="diff-line-num old old_line" data-linenumber="157" 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">
157
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<td class="diff-line-num new_line old" data-linenumber="116" 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="LC157" class="line" lang="cpp"> <span class="s" style="color: #d14;">"unable to create file %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;">out_path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="p">}</span></span>
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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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161
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<pre style="margin: 0;">-<span id="LC161" 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;">sequences</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">-<span id="LC162" 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;">quality</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="diff-line-num old old_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</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;">%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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</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;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">c_str</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;">quality</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">chunk_number</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">ofs</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span 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;">ofs</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="s" style="color: #d14;">"[rampler::Sampler::subsample] error: unable to create file on disk!"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NOLINT</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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174
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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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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"> <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;">status</span><span class="p">)</span> <span class="p">{</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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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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122
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<pre style="margin: 0;">+<span id="LC122" 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;">sequences</span><span class="p">)</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="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;">quality</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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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <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;">data</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <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;">data</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <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;">quality</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">ofs</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace rampler</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#2cd5061c4a1435b3df4eaa647d4dac4e157ae489"><strong>src/sampler.hpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file sampler.hpp</span></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @brief Sampler class header 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="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Copyright (c) 2021 Robert Vaser</span></span>
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<pre style="margin: 0;"> <span id="LC2" 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;">#pragma once</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef RAMPLER_SAMPLER_HPP_</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define RAMPLER_SAMPLER_HPP_</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdint></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">bioparser</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC14" 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="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Parser</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/parser.hpp"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "biosoup/sequence.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">rampler</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC15" 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">@@ -21,27 +17,36 @@ class Sampler;</td>
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<pre style="margin: 0;"> <span id="LC17" 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;">Sampler</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">createSampler</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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<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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Sampler</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Sampler</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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;">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;">biosoup</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;">sparser</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <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;">base_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <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;">extension</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initialize</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="p">(</span><span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</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="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">subsample</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;">out_directory</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">reference_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">coverage</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Sampler</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </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="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">out_directory</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">chunk_size</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Initialize</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</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;">Sampler</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">createSampler</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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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</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;">unique_ptr</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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sparser</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <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;">base_name</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;">extension</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">Sampler</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sampler</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Subsample</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <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;">out_directory</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">reference_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">coverage</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC41" 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;">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;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sparser_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">string</span> <span class="n" style="color: #333;">base_name_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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;">string</span> <span class="n" style="color: #333;">extension_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Split</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;">out_directory</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chunk_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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;">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;">biosoup</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;">sparser_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">sequences_length_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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;">string</span> <span class="n" style="color: #333;">base_name_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" 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;">string</span> <span class="n" style="color: #333;">extension_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace rampler</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // RAMPLER_SAMPLER_HPP_</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#33989c7ff155a4fed2047c4702a802ca716cb582"><strong>src/sequence.cpp</strong>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file sequence.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @brief Sequence class 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 "sequence.hpp"</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="LC9" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">rampler</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">name_length</span><span class="p">,</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;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">data_length</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">name_</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">),</span> <span class="n" style="color: #333;">data_</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">data_length</span><span class="p">),</span> <span class="n" style="color: #333;">quality_</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">name_length</span><span class="p">,</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;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">data_length</span><span class="p">,</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;">quality</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">quality_length</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">name_</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">),</span> <span class="n" style="color: #333;">data_</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">data_length</span><span class="p">),</span> <span class="n" style="color: #333;">quality_</span><span class="p">(</span><span class="n" style="color: #333;">quality</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">quality_length</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rampler/-/commit/6976c32e26f29994e1705bb04742b57abac625af#a62fd960b6b8c160d72e606a91e4a97b02f07bcf"><strong>src/sequence.hpp</strong>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file sequence.hpp</span></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @brief Sequence class header 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;">#pragma once</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="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">bioparser</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC13" 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="LC14" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaParser</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC16" 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="LC17" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqParser</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">rampler</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Sequence</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">default</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <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;">name</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <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;">data</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <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;">quality</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">quality_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</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="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="n" style="color: #333;">bioparser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastqParser</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="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">Sequence</span><span class="p">(</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">name_length</span><span class="p">,</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;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">data_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">Sequence</span><span class="p">(</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">name_length</span><span class="p">,</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;">data</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">data_length</span><span class="p">,</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;">quality</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">quality_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC48" 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;">string</span> <span class="n" style="color: #333;">name_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" 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;">string</span> <span class="n" style="color: #333;">data_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" 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;">string</span> <span class="n" style="color: #333;">quality_</span><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>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="p">}</span></span></pre>
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