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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libbioparser-dev">Debian Med / libbioparser-dev</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4">e20f3084</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-03-08T17:10:31+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.13</pre>
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<h4>10 changed files:</h4>
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<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
.gitmodules
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<a href="#081e63671a777defba91ae1fd2c6f5df4dfbb25b">
<span class="new-file">
+
Config.cmake.in
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#61aa04f936e09df5525dec75c3d5afd7db77eb50">
test/fasta_parser_test.cpp
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<a href="#f69ea89e2ff06e27314fd827e1ec2010bc34af71">
test/fastq_parser_test.cpp
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<a href="#1493fa78c4e1b3cb589e5feb1b2c0c9bf3088dff">
test/mhap_parser_test.cpp
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<a href="#11dc0a0e82e1a566c9bac117ae4be2cabc4326d1">
test/paf_parser_test.cpp
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<a href="#2ae985f73f0e4a0ac716c9aacafca937192edbf8">
test/sam_parser_test.cpp
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<h4>Changes:</h4>
<li id="7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44"><strong>.gitmodules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">[submodule "vendor/biosoup"]</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> path = vendor/biosoup</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> url = https://github.com/rvaser/biosoup</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<td class="new_line diff-line-num" data-linenumber="3" 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">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num" data-linenumber="4" 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<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.<span class="idiff left right">9.2</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GCC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">4.8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># GCC 4.8.5 & CMake 3.<span class="idiff left right">12.4</span></span></span>
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<td class="new_line diff-line-num" data-linenumber="6" 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="new_line diff-line-num new" 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="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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<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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=gcc-4.8 && export CXX=g++-4.8"</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.5</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 3.5.<span class="idiff left">0</span> & CMake 3.<span class="idiff right">9.2</span></span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Clang</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.5</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(Linux)"</span> <span class="c1" style="color: #998; font-style: italic;"># Clang 3.5.<span class="idiff left">2</span> & CMake 3.<span class="idiff right">12.4</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-trusty-3.5</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.5</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>
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<pre style="margin: 0;"> <span id="LC24" 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="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">SET_COMPILER="export CC=clang-3.5 && export CXX=clang++-3.5"</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"></span>
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<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.<span class="idiff left">0</span></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.<span class="idiff">0.0</span> & CMake 3.<span class="idiff right">9.2</span></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="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.<span class="idiff left">4</span></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.<span class="idiff">4.1</span> & CMake 3.<span class="idiff right">15.5</span></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<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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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode9<span class="idiff left right">.4</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${SET_COMPILER}"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build && git checkout 703bd9c</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_CXX_FLAGS="-std=c++11" .. && make && sudo make install</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd ../../</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build && cd build</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake <span class="idiff left right">-Dbioparser_build_tests=ON </span>-DCMAKE_BUILD_TYPE=Release .. && make</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=Release .. && make</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./bin/bioparser_test</span></span>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#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.<span class="idiff left right">9</span><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.<span class="idiff left right">11</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bioparser VERSION 3.0.1<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bioparser VERSION 3.0.1<span class="idiff left right">3</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"> LANGUAGES CXX</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"> DESCRIPTION <span class="s2" style="color: #d14;">"Bioparser is a c++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,31 +13,108 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_LIBRARY_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</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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<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;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB REQUIRED<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> INTERFACE<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;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> INTERFACE</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cmake"> ZLIB::ZLIB<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>bioparser_main_project ON<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>bioparser_install <span class="s2" style="color: #d14;">"Generate install target"</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">bioparser_main_project</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>bioparser_build_tests <span class="s2" style="color: #d14;">"Build unit tests"</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">bioparser_main_project</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> INTERFACE</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB 1.2.8 REQUIRED<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>bioparser_build_tests <span class="s2" style="color: #d14;">"Build bioparser unit tests"</span> OFF<span class="p">)</span></span>
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25
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>bioparser_build_tests<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>GTest REQUIRED<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET biosoup<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>vendor/biosoup EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>biosoup 0.10.0 QUIET<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>GTest 1.10.0 QUIET<span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT biosoup_FOUND<span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>FetchContent<span class="p">)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"> biosoup</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/rvaser/biosoup</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cmake"> GIT_TAG 0.10.0<span class="p">)</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>biosoup<span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT biosoup_POPULATED<span class="p">)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>biosoup<span class="p">)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">biosoup_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">biosoup_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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29
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_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>_test</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cmake"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT GTest_FOUND<span class="p">)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>FetchContent<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Declare</span><span class="p">(</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cmake"> googletest</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cmake"> GIT_REPOSITORY https://github.com/google/googletest</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cmake"> GIT_TAG release-1.10.0<span class="p">)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cmake"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_GetProperties</span><span class="p">(</span>googletest<span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT googletest_POPULATED<span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">FetchContent_Populate</span><span class="p">(</span>googletest<span class="p">)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">googletest_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">googletest_BINARY_DIR</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cmake"> EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>GTest::Main ALIAS gtest_main<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span>bioparser INTERFACE<span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_library</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>::bioparser ALIAS bioparser<span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cmake"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_include_directories</span><span class="p">(</span>bioparser INTERFACE</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cmake"> $<BUILD_INTERFACE:<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cmake"> $<INSTALL_INTERFACE:include><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>bioparser INTERFACE</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cmake"> ZLIB::ZLIB<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>bioparser_install<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>GNUInstallDirs<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CMakePackageConfigHelpers<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">configure_package_config_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/Config.cmake.in</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>Config.cmake</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"> INSTALL_DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span>/cmake/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">write_basic_package_version_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>ConfigVersion.cmake</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cmake"> COMPATIBILITY SameMajorVersion<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cmake"> TARGETS bioparser</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cmake"> EXPORT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>Targets<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cmake"> DIRECTORY include/bioparser</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_INCLUDEDIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cmake"> EXPORT <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>Targets</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cmake"> NAMESPACE <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>::</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span>/cmake/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">install</span><span class="p">(</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cmake"> FILES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>Config.cmake</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>ConfigVersion.cmake</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_LIBDIR</span><span class="si" style="color: #d14;">}</span>/cmake/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</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="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cmake"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>bioparser_build_tests<span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bioparser_test</span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cmake"> test/parser_test.cpp</span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cmake"> test/fasta_parser_test.cpp</span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cmake"> test/fastq_parser_test.cpp</span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cmake"> test/mhap_parser_test.cpp</span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cmake"> test/paf_parser_test.cpp</span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cmake"> test/sam_parser_test.cpp<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_test</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cmake"> biosoup</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cmake"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>bioparser_test</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cmake"> bioparser</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cmake"> biosoup::biosoup</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cmake"> GTest::Main<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_test PRIVATE</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cmake"> BIOPARSER_DATA_PATH=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/test/data/"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_compile_definitions</span><span class="p">(</span>bioparser_test</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cmake"> PRIVATE TEST_DATA=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/test/data/"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#081e63671a777defba91ae1fd2c6f5df4dfbb25b"><strong>Config.cmake.in</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@PACKAGE_INIT@</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">include(CMakeFindDependencyMacro)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">find_dependency(ZLIB)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@Targets.cmake")</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">check_required_components("@PROJECT_NAME@")</span></pre>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,28 +3,47 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Latest GitHub release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/rvaser/bioparser.svg</span><span class="p">)</span>](https://github.com/rvaser/bioparser/releases/latest)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status for gcc/clang</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.com/rvaser/bioparser.svg?branch=master</span><span class="p">)</span>](https://travis-ci.com/rvaser/bioparser)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">Bioparser is a c++ header only parsing library for several <span class="idiff left right">formats in </span>bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">Bioparser is a c++ header only parsing library for several bioinformatics <span class="idiff left right">formats </span>(FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<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">If you would like to add bioparser to your project via CMake, add the following:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">To build bioparser 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 https://github.com/rvaser/bioparser <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>bioparser <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="LC13" 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="LC14" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">which will create install targets and unit tests. Running <span class="sb" style="color: #d14;">`make install`</span> will create a package on your system that can be searched and linked with:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">```</span><span class="nl">cmake</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>bioparser<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><target> bioparser::bioparser<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">On the other hand, you can include bioparser as a submodule and add it to your project with the following:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">```</span><span class="nl">cmake</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TARGET bioparser<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span><path_to_submodules>/bioparser EXCLUDE_FROM_ALL<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><<span class="idiff left right">your_exe> </span>bioparser<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><<span class="idiff left right">target> bioparser::</span>bioparser<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">If you are not using CMake, include the appropriate header file directly to your project and link with zlib.</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="gu" style="color: #800080; font-weight: 600;">#### Build options</span></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="p">-</span> <span class="sb" style="color: #d14;">`bioparser_install`</span>: generate install target</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">-</span> <span class="sb" style="color: #d14;">`bioparser_build_tests`</span>: build unit tests</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="gu" style="color: #800080; font-weight: 600;">#### Dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="p">-</span> gcc 4.8+ or clang 3.5+</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p">-</span> (optional) cmake 3.9+</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="p">-</span> zlib</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">-</span> gcc 4.8+ | clang 3.5+</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">-</span> zlib 1.2.8+</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">-</span> (optional) cmake 3.11+</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###### Hidden</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) biosoup 0.10.0</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">-</span> (bioparser_test) googletest 1.10.0</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Examples</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### FASTA parser</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">#</span> FASTA parser</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/fasta_parser.hpp"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +62,7 @@ auto p = bioparser::Parser<Sequence>::Create<bioparser::FastaParser>(path);</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### FASTQ parser</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">#</span> FASTQ parser</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/fastq_parser.hpp"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,16 +80,19 @@ auto p = bioparser::Parser<Sequence>::Create<bioparser::FastqParser>(path);</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="c1" style="color: #998; font-style: italic;">// parse in chunks</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><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;">s</span><span class="p">;</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"><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="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</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;">// 500 MB</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</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 class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><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="LC84" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</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 class="c1" style="color: #998; font-style: italic;">// 1 GB</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</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="LC86" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">t</span></span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">t</span></span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()));</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">c</span></span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_move_iterator</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">c</span></span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()));</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### MHAP parser</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">#</span> MHAP parser</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/mhap_parser.hpp"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,7 +121,7 @@ auto p = bioparser::Parser<Overlap>::Create<bioparser::MhapParser>(path);</td>
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99
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### PAF parser</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">#</span> PAF parser</span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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105
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/paf_parser.hpp"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,7 +150,7 @@ auto p = bioparser::Parser<Overlap>::Create<bioparser::PafParser>(path);</td>
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128
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Parse</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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129
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### SAM parser</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right">#</span> SAM parser</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/sam_parser.hpp"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,20 +188,6 @@ friend bioparser::PafParser<Overlap>;</td>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"><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;">SamParser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Overlap</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Unit tests</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="markdown">To build and run bioparser unit tests run the following commands:</span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="markdown">git clone <span class="nt" style="color: #000080;">--recursive</span> https://github.com/rvaser/bioparser.git bioparser</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>bioparser <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="LC176" class="line" lang="markdown">cmake <span class="nt" style="color: #000080;">-Dbioparser_build_tests</span><span class="o" style="font-weight: 600;">=</span>ON <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="LC177" class="line" lang="markdown">./bin/bioparser_test</span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC180" 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="LC181" class="line" lang="markdown"><span class="p">-</span> gtest</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Acknowledgement</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown">This work has been supported in part by the Croatian Science Foundation under the project Single genome and metagenome assembly (IP-2018-01-5886).</span></pre>
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<li id="61aa04f936e09df5525dec75c3d5afd7db77eb50">
<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#61aa04f936e09df5525dec75c3d5afd7db77eb50"><strong>test/fasta_parser_test.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ namespace test {</td>
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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;">BioparserFastaTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="nl">public:</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;">void</span> <span class="n" style="color: #333;">Setup</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;">file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">BIOPARSER_DATA_PATH</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">file</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// NOLINT</span></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">FastaParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_DATA</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">file</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <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;">void</span> <span class="n" style="color: #333;">Check</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#f69ea89e2ff06e27314fd827e1ec2010bc34af71"><strong>test/fastq_parser_test.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ namespace test {</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BioparserFastqTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Setup</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;">file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">FastqParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">BIOPARSER_DATA_PATH</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">file</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// NOLINT</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">FastqParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">TEST_DATA</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">file</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Check</span><span class="p">()</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#1493fa78c4e1b3cb589e5feb1b2c0c9bf3088dff"><strong>test/mhap_parser_test.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ struct MhapOverlap: public biosoup::Overlap {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BioparserMhapTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Setup</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;">file</span><span class="p">)</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;">p</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;">MhapOverlap</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;">MhapParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">BIOPARSER_DATA_PATH</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</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;">p</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;">MhapOverlap</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;">MhapParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">TEST_DATA</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</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>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Check</span><span class="p">()</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#11dc0a0e82e1a566c9bac117ae4be2cabc4326d1"><strong>test/paf_parser_test.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +49,7 @@ struct PafOverlap: public biosoup::Overlap {</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BioparserPafTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Setup</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;">file</span><span class="p">)</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;">p</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;">PafOverlap</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;">PafParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">BIOPARSER_DATA_PATH</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</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;">p</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;">PafOverlap</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;">PafParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">TEST_DATA</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</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="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Check</span><span class="p">()</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/e20f3084a5916994eaf3b1f784aff2f9584bc2e4#2ae985f73f0e4a0ac716c9aacafca937192edbf8"><strong>test/sam_parser_test.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ struct SamOverlap: public biosoup::Overlap {</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BioparserSamTest</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Test</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Setup</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;">file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">SamOverlap</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;">SamParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">BIOPARSER_DATA_PATH</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">p</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;">SamOverlap</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;">SamParser</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">TEST_DATA</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Check</span><span class="p">()</span> <span class="p">{</span></span>
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