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GitLab

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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/gatb-core">Debian Med / gatb-core</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e">d6238780</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-12-04T23:22:52Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.1+git20191130.664696c+dfsg</pre>

</li>

</ul>

<h4>24 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#4c007bda60857aed5186f73b4dd88ee753952d0d">

gatb-core/CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#2fba22cc64bca97d995e238b012045ac90567b80">

gatb-core/doc/doxygen/src/dbgh5page.hpp

</a>

</li>

<li class="file-stats">

<a href="#6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33">

gatb-core/src/gatb/bank/impl/BankFasta.cpp

</a>

</li>

<li class="file-stats">

<a href="#490f86cdfc07e7db3455fffd8859052bd5dbeb50">

gatb-core/src/gatb/bcalm2/bglue_algo.cpp

</a>

</li>

<li class="file-stats">

<a href="#349369b0ff3f84575fe0d9513fb9bfcadb1b3612">

gatb-core/src/gatb/bcalm2/bglue_algo.hpp

</a>

</li>

<li class="file-stats">

<a href="#fa53c8abddac2ffbd797f8ad40c9772134223fed">

gatb-core/src/gatb/debruijn/impl/Graph.cpp

</a>

</li>

<li class="file-stats">

<a href="#2ff315124cb4ed9eebb9d35c35743144de29a781">

gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp

</a>

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<li class="file-stats">

<a href="#34ae9ab374303a1000194fa7d58aeba9d58f32ce">

gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp

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<li class="file-stats">

<a href="#8d46876b0b01c8687ffec95a3e56a84f1d5ffc83">

gatb-core/src/gatb/debruijn/impl/LinkTigs.hpp

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<li class="file-stats">

<a href="#47e6fff3caa93f4ef7cc54b7f08ec8ac25b21393">

gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp

</a>

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<li class="file-stats">

<a href="#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4">

gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp

</a>

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<li class="file-stats">

<a href="#6dc8c95d8c6c04e96a48b4cf5c3c2ea31cc93750">

gatb-core/src/gatb/system/impl/FileSystemCommon.hpp

</a>

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<li class="file-stats">

<a href="#4c12716c6fcb516eda353ab99ab2b81002b77515">

gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in

</a>

</li>

<li class="file-stats">

<a href="#9be95217b1b4429f2eeabc2213c457fd389f08a0">

gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp

</a>

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<li class="file-stats">

<a href="#4ae6c527aafe52f4f16907962f525902d4b5ef6f">

gatb-core/src/gatb/tools/misc/api/StringsRepository.hpp

</a>

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<li class="file-stats">

<a href="#3b8fda1a420e311e4fb4b0d9fe344d4bbc2f4e97">

gatb-core/src/gatb/tools/misc/impl/Tool.cpp

</a>

</li>

<li class="file-stats">

<a href="#f84f48b86f89b6fe6f3b401f6ed674d1ffab829b">

gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp

</a>

</li>

<li class="file-stats">

<a href="#9e0109d139212f56eef6153e59e64fa4c6670360">

gatb-core/src/gatb/tools/storage/impl/Storage.hpp

</a>

</li>

<li class="file-stats">

<a href="#efdf123a4ecf95f1a9326ff6d3443694ceed944f">

gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp

</a>

</li>

<li class="file-stats">

<a href="#dd31cf0d08329fcf5ce3e2647df00c99baa267ba">

gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp

</a>

</li>

<li class="file-stats">

<a href="#d7401b2bb5a2b6245ce8cd38b4b1c20e7ea1a058">

gatb-core/test/unit/src/debruijn/TestDebruijn.cpp

</a>

</li>

<li class="file-stats">

<a href="#49ce0c04f76f93b18c25528d056dc803569026e0">

gatb-core/test/unit/src/kmer/TestDSK.cpp

</a>

</li>

<li class="file-stats">

<a href="#e2e4e0dc5c61805b798db5e2dee529b92e327235">

gatb-core/test/unit/src/tools/storage/TestStorage.cpp

</a>

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<li class="file-stats">

<a href="#e79cab2022b11c71b2d8095f0ebe49260b3cc139">

<span class="new-file">

+

gatb-core/thirdparty/update-boost.sh

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="4c007bda60857aed5186f73b4dd88ee753952d0d">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#4c007bda60857aed5186f73b4dd88ee753952d0d"><strong>gatb-core/CMakeLists.txt</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="110" 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">@@ -110,8 +110,6 @@ if (debug)</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cmake">    <span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>LIBRARY_COMPILE_DEFINITIONS  <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARY_COMPILE_DEFINITIONS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -g -p </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIB_COMPILE_WARNINGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="111" 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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<td class="diff-line-num new_line" data-linenumber="111" 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="LC111" class="line" lang="cmake">    <span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>CMAKE_BUILD_TYPE Debug<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># else CMake adds DNDEBUG</span></span>

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<td class="diff-line-num old_line" data-linenumber="112" 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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<td class="diff-line-num new_line" data-linenumber="112" 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="LC112" class="line" lang="cmake">    <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"-- COMPILATION IN DEBUG MODE"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cmake">    <span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>LIBRARY_COMPILE_DEFINITIONS  <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARY_COMPILE_DEFINITIONS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -O3 -DNDEBUG </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIB_COMPILE_WARNINGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>

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<td class="diff-line-num old_line" data-linenumber="116" 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="LC114" class="line" lang="cmake"></span>

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<td class="diff-line-num old_line" data-linenumber="117" 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="LC115" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>INT128_FOUND<span class="p">)</span></span>

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</li>

<li id="2fba22cc64bca97d995e238b012045ac90567b80">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#2fba22cc64bca97d995e238b012045ac90567b80"><strong>gatb-core/doc/doxygen/src/dbgh5page.hpp</strong></a>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">          -verbose           (1 arg) :    verbosity level  [default '1']</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">          -email             (1 arg) :    send statistics to the given email address  [default '']</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">          -email-fmt         (1 arg) :    'raw' or 'xml'  [default 'raw']</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">          -edge-km           (1 arg) :    Kececioglu-Myers edge representation  [default '0']</span></span>

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<td class="diff-line-num new old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>

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<td class="diff-line-num new_line" data-linenumber="96" 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="LC96" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \endcode</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num old_line" data-linenumber="96" 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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<td class="diff-line-num new_line" data-linenumber="98" 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="LC98" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<br>

</li>

<li id="6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33"><strong>gatb-core/src/gatb/bank/impl/BankFasta.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" 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="651" 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">@@ -651,6 +651,7 @@ void BankFasta::Iterator::init ()</td>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">buffered_file_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span>  <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">buffered_file_t</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp">        <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span>  <span class="n" style="color: #333;">MALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">BUFFER_SIZE</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp">        <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span> <span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp">        <span class="n" style="color: #333;">gzbuffer</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stream</span><span class="p">,</span><span class="mi" style="color: #099;">2</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>

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp">          </span>

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We check that we can open the file. */</span></span>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

</pre>

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</li>

<li id="490f86cdfc07e7db3455fffd8859052bd5dbeb50">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#490f86cdfc07e7db3455fffd8859052bd5dbeb50"><strong>gatb-core/src/gatb/bcalm2/bglue_algo.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" 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="63" 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">@@ -63,12 +63,9 @@ using namespace gatb::core::tools::collections::impl;</td>

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63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="64" 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="LC64" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="65" 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="LC65" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// let's be clear here:</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// UF hashes will be stored in 32 bits for efficiency (as I don't want to have a 64-bits UF for memory reasons, also, would require to modify unionFind.hpp)</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">uf_hashes_t</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// but there can be more than 2^{32} sequences in the glue file</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">uf_hashes_t</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// UF hashes are the hash values of k-mers to be inserted into the UF data structure. Don't try setting to uint32_t, would be a disaster</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">seq_idx_t</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// so, potentially, more than 2^{32} UF hashes (but not necessarily, consider that some sequences don't need to be glued)</span></span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// what will happen is that more one UF class won't be linked to a single unitig, but multiple unitigs</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">uf_class_t</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// UF class is the identifier of an element in the UF</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// let's hope that there won't be saturation (only 1 UF class with all unitigs)</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if this happens, then "Top 10 glue partitions by size:" will show only one entry and BCALM will blow up in memory</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// a fix would be to use a 64 bits UF (to be coded later)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" 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="194" 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">@@ -197,6 +194,24 @@ static string skip_first_abundance(const string& list)</td>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">make_header</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">abundances</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">all_abundance_counts</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">header</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mean_abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_mean_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">sum_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sum_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">all_abundance_counts</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// in this setting, all kmer wabundances are printed in the order of the kmers in the sequence</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">        <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"LN:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">seq_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ab:Z:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">abundances</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// km is not a standard GFA field so i'm putting it in lower case as per the spec</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">        <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"LN:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">seq_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" KC:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">sum_abundances</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" km:f:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string_with_precision</span><span class="p">(</span><span class="n" style="color: #333;">mean_abundance</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">header</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">markedSeq</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="699" 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">@@ -699,6 +714,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="699" 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">

699

</td>

<td class="diff-line-num new_line" data-linenumber="714" 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">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="700" 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">

700

</td>

<td class="diff-line-num new_line" data-linenumber="715" 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">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_glue_partitions</span><span class="p">,</span> </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="701" 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">

701

</td>

<td class="diff-line-num new_line" data-linenumber="716" 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">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> </span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="702" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="717" 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">

717

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">all_abundance_counts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="702" 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">

702

</td>

<td class="diff-line-num new_line" data-linenumber="718" 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">

718

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="703" 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">

703

</td>

<td class="diff-line-num new_line" data-linenumber="719" 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">

719

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp">        <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="704" 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">

704

</td>

<td class="diff-line-num new_line" data-linenumber="720" 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">

720

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="804" 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="820" 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">@@ -804,7 +820,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="804" 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">

804

</td>

<td class="diff-line-num new_line" data-linenumber="820" 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">

820

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="805" 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">

805

</td>

<td class="diff-line-num new_line" data-linenumber="821" 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">

821

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="806" 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">

806

</td>

<td class="diff-line-num new_line" data-linenumber="822" 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">

822

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<pre style="margin: 0;"> <span id="LC822" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// create a UF data structure</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

807

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC807" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// this one stores nb_uf_keys * uint64_t (actually, atomic's).<span class="idiff left right"> so it's bigger than uf_hashes</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="808" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="823" 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">

823

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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// this one stores nb_uf_keys * uint64_t (actually, atomic's).</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="808" 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">

808

</td>

<td class="diff-line-num new_line" data-linenumber="824" 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">

824

</td>

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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp">    <span class="n" style="color: #333;">unionFind</span> <span class="n" style="color: #333;">ufkmers</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="809" 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">

809

</td>

<td class="diff-line-num new_line" data-linenumber="825" 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">

825

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="810" 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">

810

</td>

<td class="diff-line-num new_line" data-linenumber="826" 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">

826

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="911" 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="927" 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">@@ -911,13 +927,13 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="911" 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">

911

</td>

<td class="diff-line-num new_line" data-linenumber="927" 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">

927

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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_uf</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// for debugging</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="912" 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">

912

</td>

<td class="diff-line-num new_line" data-linenumber="928" 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">

928

</td>

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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="913" 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">

913

</td>

<td class="diff-line-num new_line" data-linenumber="929" 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">

929

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

914

</td>

<td class="diff-line-num new_line old" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC914" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/* now we're mirroring the UF to a vector of uint32_t's, it will take less space, and strictly same information</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="915" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="930" 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">

930

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/* now we're mirroring the UF to a vector of uint32_t's<span class="idiff left right"> (uf_class_t)</span>, it will take less space, and strictly same information</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="915" 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">

915

</td>

<td class="diff-line-num new_line" data-linenumber="931" 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">

931

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * this is to get rid of the rank (one uint32) per element in the current UF implementation. </span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="916" 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">

916

</td>

<td class="diff-line-num new_line" data-linenumber="932" 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">

932

</td>

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<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * To do this, we're using the disk to save space of populating one vector from the other in memory. </span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="917" 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">

917

</td>

<td class="diff-line-num new_line" data-linenumber="933" 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">

933

</td>

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<pre style="margin: 0;"> <span id="LC933" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * (saves having to allocate both vectors at the same time) */</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="918" 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">

918

</td>

<td class="diff-line-num new_line" data-linenumber="934" 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">

934

</td>

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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp">    </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

919

</td>

<td class="diff-line-num new_line old" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC919" class="line" lang="cpp">    <span class="n" style="color: #333;">BagFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left">hashes_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bagf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">uf_hashe</span>s_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span>  <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

920

</td>

<td class="diff-line-num new_line old" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC920" class="line" lang="cpp">  <span class="n" style="color: #333;">BagCache</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left">hashes_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagCache</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">uf_hashe</span>s_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span>  <span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span> <span class="p">);</span>   <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bag</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="921" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="935" 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">

935

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp">    <span class="n" style="color: #333;">BagFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left">class_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bagf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">uf_clas</span>s_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span>  <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="921" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="936" 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">

936

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp">  <span class="n" style="color: #333;">BagCache</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left">class_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagCache</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff right">uf_clas</span>s_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span>  <span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span> <span class="p">);</span>   <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bag</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="921" 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">

921

</td>

<td class="diff-line-num new_line" data-linenumber="937" 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">

937

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC937" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="922" 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">

922

</td>

<td class="diff-line-num new_line" data-linenumber="938" 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">

938

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC938" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_uf_keys</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="923" 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">

923

</td>

<td class="diff-line-num new_line" data-linenumber="939" 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">

939

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//ufkmers_vector[i] = ufkmers.find(i); // just in-memory without the disk</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="930" 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="946" 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">@@ -930,15 +946,15 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="930" 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">

930

</td>

<td class="diff-line-num new_line" data-linenumber="946" 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">

946

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC946" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="931" 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">

931

</td>

<td class="diff-line-num new_line" data-linenumber="947" 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">

947

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC947" class="line" lang="cpp">    <span class="n" style="color: #333;">ufkmers_bag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="932" 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">

932

</td>

<td class="diff-line-num new_line" data-linenumber="948" 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">

948

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC948" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

933

</td>

<td class="diff-line-num new_line old" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC933" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left right">hashe</span>s_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_vector</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

934

</td>

<td class="diff-line-num new_line old" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC934" class="line" lang="cpp">    <span class="n" style="color: #333;">IteratorFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left right">hashe</span>s_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="935" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="949" 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">

949

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left right">clas</span>s_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_vector</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="935" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="950" 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">

950

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp">    <span class="n" style="color: #333;">IteratorFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_<span class="idiff left right">clas</span>s_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="935" 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">

935

</td>

<td class="diff-line-num new_line" data-linenumber="951" 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">

951

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC951" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="936" 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">

936

</td>

<td class="diff-line-num new_line" data-linenumber="952" 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">

952

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC952" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="937" 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">

937

</td>

<td class="diff-line-num new_line" data-linenumber="953" 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">

953

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp">            <span class="n" style="color: #333;">ufkmers_vector</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">item</span><span class="p">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="938" 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">

938

</td>

<td class="diff-line-num new_line" data-linenumber="954" 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">

954

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="939" 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">

939

</td>

<td class="diff-line-num new_line" data-linenumber="955" 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">

955

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp">    <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="940" 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">

940

</td>

<td class="diff-line-num new_line" data-linenumber="956" 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">

956

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

941

</td>

<td class="diff-line-num new_line old" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded 32-bit UF ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uf_<span class="idiff left right">hashe</span>s_t</span><span class="p">)</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="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="942" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="957" 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">

957

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded 32-bit UF ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uf_<span class="idiff left right">clas</span>s_t</span><span class="p">)</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="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="942" 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">

942

</td>

<td class="diff-line-num new_line" data-linenumber="958" 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">

958

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC958" class="line" lang="cpp">  </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="943" 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">

943

</td>

<td class="diff-line-num new_line" data-linenumber="959" 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">

959

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC959" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// setup output file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="944" 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">

944

</td>

<td class="diff-line-num new_line" data-linenumber="960" 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">

960

</td>

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<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1000" 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="1016" 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">@@ -1000,7 +1016,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1000" 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">

1000

</td>

<td class="diff-line-num new_line" data-linenumber="1016" 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">

1016

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1016" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1001" 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">

1001

</td>

<td class="diff-line-num new_line" data-linenumber="1017" 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">

1017

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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// partition the glue into many files, à la dsk</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1002" 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">

1002

</td>

<td class="diff-line-num new_line" data-linenumber="1018" 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">

1018

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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">partitionGlue</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modelCanon</span> <span class="cm" style="color: #998; font-style: italic;">/* crashes if copied!*/</span><span class="p">,</span> \</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1003

</td>

<td class="diff-line-num new_line old" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1003" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_UFclass</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gluePartitions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1004" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1019" 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">

1019

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_UFclass</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gluePartitions</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">all_abundance_counts</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1004" 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">

1004

</td>

<td class="diff-line-num new_line" data-linenumber="1020" 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">

1020

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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outLock</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_seqs_in_partition</span><span class="p">,</span> <span class="n" style="color: #333;">nbGluePartitions</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1005" 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">

1005

</td>

<td class="diff-line-num new_line" data-linenumber="1021" 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">

1021

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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp">            <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1006" 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">

1006

</td>

<td class="diff-line-num new_line" data-linenumber="1022" 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">

1022

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1024" 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="1040" 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">@@ -1024,11 +1040,8 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1024" 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">

1024

</td>

<td class="diff-line-num new_line" data-linenumber="1040" 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">

1040

</td>

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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found_class</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// this one doesn't need to be glued</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1025" 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">

1025

</td>

<td class="diff-line-num new_line" data-linenumber="1041" 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">

1041

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1026" 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">

1026

</td>

<td class="diff-line-num new_line" data-linenumber="1042" 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">

1042

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1027

</td>

<td class="diff-line-num new_line old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1027" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mean_abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_mean_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1028

</td>

<td class="diff-line-num new_line old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">sum_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sum_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1029

</td>

<td class="diff-line-num new_line old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp">            </span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1030

</td>

<td class="diff-line-num new_line old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// km is not a standard GFA field so i'm putting it in lower case as per the spec</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1031

</td>

<td class="diff-line-num new_line old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cpp">            <span class="n" style="color: #333;">output</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"LN:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" KC:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">sum_abundances</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" km:f:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string_with_precision</span><span class="p">(</span><span class="n" style="color: #333;">mean_abundance</span><span class="p">));</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1032" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1043" 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">

1043

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_header</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span><span class="n" style="color: #333;">abundances</span><span class="p">,</span> <span class="n" style="color: #333;">all_abundance_counts</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1032" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1044" 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">

1044

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp">            <span class="n" style="color: #333;">output</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">);</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1032" 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">

1032

</td>

<td class="diff-line-num new_line" data-linenumber="1045" 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">

1045

</td>

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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1033" 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">

1033

</td>

<td class="diff-line-num new_line" data-linenumber="1046" 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">

1046

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1034" 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">

1034

</td>

<td class="diff-line-num new_line" data-linenumber="1047" 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">

1047

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1082" 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="1095" 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">@@ -1082,7 +1095,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1082" 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">

1082

</td>

<td class="diff-line-num new_line" data-linenumber="1095" 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">

1095

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1095" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">partition</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">partition</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nbGluePartitions</span><span class="p">;</span> <span class="n" style="color: #333;">partition</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1083" 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">

1083

</td>

<td class="diff-line-num new_line" data-linenumber="1096" 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">

1096

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1096" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1084" 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">

1084

</td>

<td class="diff-line-num new_line" data-linenumber="1097" 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">

1097

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1097" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">glue_partition</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modelCanon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ufkmers</span><span class="p">,</span> <span class="n" style="color: #333;">partition</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gluePartition_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">nbGluePartitions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">copy_nb_seqs_in_partition</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1085

</td>

<td class="diff-line-num new_line old" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1085" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_UFclass</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outLock</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">](</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_id</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1086" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1098" 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">

1098

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">get_UFclass</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outLock</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">all_abundance_counts</span></span><span class="p">](</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_id</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1086" 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">

1086

</td>

<td class="diff-line-num new_line" data-linenumber="1099" 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">

1099

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1087" 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">

1087

</td>

<td class="diff-line-num new_line" data-linenumber="1100" 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">

1100

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1088" 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">

1088

</td>

<td class="diff-line-num new_line" data-linenumber="1101" 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">

1101

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1101" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1172" 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="1185" 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">@@ -1172,10 +1185,9 @@ void bglue(Storage *storage,</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1172" 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">

1172

</td>

<td class="diff-line-num new_line" data-linenumber="1185" 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">

1185

</td>

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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp">                <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">abs</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1173" 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">

1173

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<td class="diff-line-num new_line" data-linenumber="1186" 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">

1186

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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp">                <span class="n" style="color: #333;">glue_sequences</span><span class="p">(</span><span class="n" style="color: #333;">seqs_to_glue</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">seqs_to_glue_is_circular</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">abundances</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">abs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// takes as input the indices of ordered sequences, whether that sequence is circular, and the markedSeq's themselves along with their abundances</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1174" 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">

1174

</td>

<td class="diff-line-num new_line" data-linenumber="1187" 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">

1187

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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1175

</td>

<td class="diff-line-num new_line old" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1175" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mean_abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_mean_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1176

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<td class="diff-line-num new_line old" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1176" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sum_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sum_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1177" 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">

1177

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<td class="diff-line-num new_line" data-linenumber="1188" 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">

1188

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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="cpp">                <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1178

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<td class="diff-line-num new_line old" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="cpp">                    <span class="n" style="color: #333;">output</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"LN:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" KC:i:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">sum_abundances</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" km:f:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string_with_precision</span><span class="p">(</span><span class="n" style="color: #333;">mean_abundance</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1179" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1189" 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">

1189

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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp">                    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_header</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span><span class="n" style="color: #333;">abs</span><span class="p">,</span> <span class="n" style="color: #333;">all_abundance_counts</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1179" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1190" 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">

1190

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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp">                    <span class="n" style="color: #333;">output</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1179" 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">

1179

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<td class="diff-line-num new_line" data-linenumber="1191" 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">

1191

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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1180" 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">

1180

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<td class="diff-line-num new_line" data-linenumber="1192" 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">

1192

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1192" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1181" 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">

1181

</td>

<td class="diff-line-num new_line" data-linenumber="1193" 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">

1193

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1193" class="line" lang="cpp">                </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1198" 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="1210" 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">@@ -1198,7 +1210,7 @@ void bglue(Storage *storage,</td>

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1198

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<td class="diff-line-num new_line" data-linenumber="1210" 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">

1210

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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1199" 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">

1199

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<td class="diff-line-num new_line" data-linenumber="1211" 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">

1211

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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"end"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1200" 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">

1200

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<td class="diff-line-num new_line" data-linenumber="1212" 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">

1212

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1212" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1201

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<td class="diff-line-num new_line old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug_keep_glue_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">true</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">// for debugging // TODO enable it if -redo-bglue param was provided (need some info from UnitigsConstructionAlgorithm). </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1202" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1213" 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">

1213

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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug_keep_glue_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</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">// for debugging // TODO warning: if debug_keep_glue_files is set to 'false,' then the debug option '-redo-bglue' cannot work because it needs those bglue files</span></span></span>

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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_keep_glue_files</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"debug: not deleting glue files"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<li id="349369b0ff3f84575fe0d9513fb9bfcadb1b3612">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#349369b0ff3f84575fe0d9513fb9bfcadb1b3612"><strong>gatb-core/src/gatb/bcalm2/bglue_algo.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -150,6 +150,7 @@ void bglue(gatb::core::tools::storage::impl::Storage* storage,</td>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> </span>

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151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_glue_partitions</span><span class="p">,</span> </span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> </span>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">all_abundance_counts</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">        <span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"></span>

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<li id="fa53c8abddac2ffbd797f8ad40c9772134223fed">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#fa53c8abddac2ffbd797f8ad40c9772134223fed"><strong>gatb-core/src/gatb/debruijn/impl/Graph.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="648" 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="648" 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">@@ -648,6 +648,8 @@ IOptionsParser* GraphTemplate<Node, Edge, GraphDataVariant>::getOptionsParser (b</td>

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648

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<td class="diff-line-num new_line" data-linenumber="648" 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="LC648" class="line" lang="cpp">    <span class="n" style="color: #333;">IOptionsParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parserGeneral</span>  <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionsParser</span> <span class="p">(</span><span class="s" style="color: #d14;">"general"</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="649" 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">

649

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<td class="diff-line-num new_line" data-linenumber="649" 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="LC649" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_INTEGER_PRECISION</span><span class="p">,</span> <span class="s" style="color: #d14;">"integers precision (0 for optimized value)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<td class="diff-line-num new_line" data-linenumber="650" 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="LC650" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_VERBOSE</span><span class="p">,</span>           <span class="s" style="color: #d14;">"verbosity level"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span>  <span class="p">));</span></span>

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<td class="diff-line-num new old_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="651" 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="LC651" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_EDGE_KM_REPRESENTATION</span><span class="p">,</span>           <span class="s" style="color: #d14;">"edge km representation"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span>  <span class="p">));</span></span>

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</td>

<td class="diff-line-num new new_line" data-linenumber="652" 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">

652

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_ALL_ABUNDANCE_COUNTS</span><span class="p">,</span>           <span class="s" style="color: #d14;">"output all k-mer abundance counts instead of mean"</span> <span class="p">));</span></span>

</pre>

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651

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<td class="diff-line-num new_line" data-linenumber="653" 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">

653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">,</span>          <span class="s" style="color: #d14;">"number of cores"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span>  <span class="p">));</span></span>

</pre>

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652

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654

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp">    <span class="n" style="color: #333;">parserGeneral</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="n" style="color: #333;">STR_CONFIG_ONLY</span><span class="p">,</span>       <span class="s" style="color: #d14;">"dump config only"</span><span class="p">));</span></span>

</pre>

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653

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<td class="diff-line-num new_line" data-linenumber="655" 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">

655

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="661" 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="663" 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">@@ -661,7 +663,7 @@ IOptionsParser* GraphTemplate<Node, Edge, GraphDataVariant>::getOptionsParser (b</td>

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<td class="diff-line-num old_line" data-linenumber="661" 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">

661

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<td class="diff-line-num new_line" data-linenumber="663" 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">

663

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-skip-links"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       skip     links"</span><span class="p">));</span></span>

</pre>

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662

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<td class="diff-line-num new_line" data-linenumber="664" 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">

664

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-redo-links"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       redo     links"</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="663" 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">

663

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<td class="diff-line-num new_line" data-linenumber="665" 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">

665

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-skip-bglue"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       skip     bglue"</span><span class="p">));</span></span>

</pre>

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664

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<td class="diff-line-num new_line old" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-redo-bglue"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       redo     bglue"</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="665" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="666" 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">

666

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-redo-bglue"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       redo     bglue<span class="idiff left right"> (needs debug_keep_glue_files=true in source code)</span>"</span><span class="p">));</span></span>

</pre>

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665

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<td class="diff-line-num new_line" data-linenumber="667" 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">

667

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-skip-bcalm"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"same, but       skip     bcalm"</span><span class="p">));</span></span>

</pre>

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666

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<td class="diff-line-num new_line" data-linenumber="668" 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">

668

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp">    <span class="n" style="color: #333;">parserDebug</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span>  <span class="p">(</span><span class="s" style="color: #d14;">"-redo-bcalm"</span><span class="p">,</span>       <span class="s" style="color: #d14;">"debug function, redo the bcalm algo"</span><span class="p">));</span></span>

</pre>

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667

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<td class="diff-line-num new_line" data-linenumber="669" 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">

669

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"></span>

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<br>

</li>

<li id="2ff315124cb4ed9eebb9d35c35743144de29a781">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#2ff315124cb4ed9eebb9d35c35743144de29a781"><strong>gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -259,7 +259,7 @@ void GraphUnitigsTemplate<span>::build_unitigs_postsolid(std::string unitigs_fil</td>

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259

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp">    <span class="p">}</span></span>

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260

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260

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">redo_bcalm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">props</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-redo-bcalm"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">redo_bglue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">props</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-redo-bglue"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">redo_bglue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">props</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-redo-bglue"</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// note: if that option is to be used, make sure to enable debug_keep_glue_files=true in bglue_algo.cpp</span></span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">redo_links</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">props</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-redo-links"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">skip_bcalm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">props</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-skip-bcalm"</span><span class="p">);</span></span>

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<br>

</li>

<li id="34ae9ab374303a1000194fa7d58aeba9d58f32ce">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#34ae9ab374303a1000194fa7d58aeba9d58f32ce"><strong>gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="52" 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">@@ -52,7 +52,7 @@ namespace gatb { namespace core { namespace debruijn { namespace impl  {</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  Normally bcalm outputs consecutive unitig ID's but LinkTigs can also work with non-consecutive, non-sorted IDs</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span></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;">link_tigs</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span></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;">link_tigs</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge_km_representation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">    <span class="n" style="color: #333;">bcalm_logging</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankFasta</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".linked"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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="60" 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">@@ -60,7 +60,7 @@ void link_tigs(string unitigs_filename, int kmerSize, int nb_threads, uint64_t &</td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"Finding links between unitigs"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" 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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<td class="diff-line-num new_line" data-linenumber="61" 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="LC61" class="line" lang="cpp"></span>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp">        <span class="n" style="color: #333;">link_unitigs_pass</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">renumber_unitigs</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" 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="LC63" class="line" lang="cpp">        <span class="n" style="color: #333;">link_unitigs_pass</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">edge_km_representation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">renumber_unitigs</span></span><span class="idiff right"> </span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="64" 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="LC64" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="65" 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="LC65" class="line" lang="cpp">    <span class="n" style="color: #333;">write_final_output</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="66" 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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<td class="diff-line-num new_line" data-linenumber="66" 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="LC66" class="line" lang="cpp">   </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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="265" 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">@@ -265,7 +265,7 @@ static void record_links(uint64_t utig_id, int pass, const string &link, std::of</td>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_unitigs_pass</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="268" 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="LC268" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_unitigs_pass</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge_km_representation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelCanonical</span> <span class="n" style="color: #333;">Model</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span>           <span class="n" style="color: #333;">Type</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="376" 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="376" 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">@@ -376,7 +376,12 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">//bool rc = e_in.rc ^ (!beginInSameOrientation); // "rc" sets the destination strand // i don't think it's the right formula because of k-1-mers that are their self revcomp. see the mikko bug in the test folder, that provides a nice illustration of that </span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp">                    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e_in</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UNITIG_END</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// a better way to determine the rc flag is just looking at position of e_in k-1-mer </span></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp">                    <span class="n" style="color: #333;">in_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"L:-:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_in</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp">                    </span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">edge_km_representation</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">                        <span class="n" style="color: #333;">in_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"J:0:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_in</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"0"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp">                    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp">                        <span class="n" style="color: #333;">in_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"L:-:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_in</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp">                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp">                    <span class="cm" style="color: #998; font-style: italic;">/* what to do when kmerBegin is same as forward and reverse?</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                     used to have this:</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">@@ -432,7 +437,13 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp">                    </span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp">                    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e_out</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UNITIG_END</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// a better way to determine the rc flag is just looking at position of e_in k-1-mer </span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp">                    <span class="n" style="color: #333;">out_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"L:+:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_out</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">edge_km_representation</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp">                        <span class="n" style="color: #333;">out_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"J:1:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_out</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"0"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp">                    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp">                        <span class="n" style="color: #333;">out_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"L:+:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">e_out</span><span class="p">.</span><span class="n" style="color: #333;">unitig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> </span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp">                    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp">                    </span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [valid] "</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp">                <span class="p">}</span></span>

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<br>

</li>

<li id="8d46876b0b01c8687ffec95a3e56a84f1d5ffc83">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#8d46876b0b01c8687ffec95a3e56a84f1d5ffc83"><strong>gatb-core/src/gatb/debruijn/impl/LinkTigs.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,10 +30,10 @@ namespace gatb { namespace core { namespace debruijn { namespace impl  {</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_tigs</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_tigs</span><span class="p">(</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge_km_representation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_unitigs_pass</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="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">renumber_unitigs</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_unitigs_pass</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="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge_km_representation</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">renumber_unitigs</span></span><span class="idiff right"> </span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="p">}}}}</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>

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<br>

</li>

<li id="47e6fff3caa93f4ef7cc54b7f08ec8ac25b21393">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#47e6fff3caa93f4ef7cc54b7f08ec8ac25b21393"><strong>gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" 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="91" 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">@@ -91,17 +91,15 @@ UnitigsConstructionAlgorithm<span>::~UnitigsConstructionAlgorithm ()</td>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UnitigsConstructionAlgorithm</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">execute</span> <span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp">    <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp">            <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_KMER_SIZE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">=</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp">            <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_KMER_ABUNDANCE_MIN</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// note: doesn't work when it's "auto"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimizerSize</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp">        <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_MINIMIZER_SIZE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp">        <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimizer_type</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp">        <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_MINIMIZER_TYPE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_VERBOSE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="cpp">    <span class="n" style="color: #333;">kmerSize</span>                    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_KMER_SIZE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span>               <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_KMER_ABUNDANCE_MIN</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// note: doesn't work when it's "auto"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" 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="LC96" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimizerSize</span>           <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_MINIMIZER_SIZE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" 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="LC97" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span>              <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimizer_type</span>          <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_MINIMIZER_TYPE</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span>                <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_VERBOSE</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">edge_km_representation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_EDGE_KM_REPRESENTATION</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="101" 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="LC101" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">all_abundance_counts</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_ALL_ABUNDANCE_COUNTS</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="102" 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="LC102" class="line" lang="cpp">   </span>

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<td class="diff-line-num new_line" data-linenumber="103" 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="LC103" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_glue_partitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" 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="LC104" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"-nb-glue-partitions"</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">        <span class="n" style="color: #333;">nb_glue_partitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="s" style="color: #d14;">"-nb-glue-partitions"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="108" 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">@@ -110,9 +108,9 @@ void UnitigsConstructionAlgorithm<span>::execute ()</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">nb_threads</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nbThreads</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Uh. Unitigs graph construction called with nb_threads "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nb_threads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" but dispatcher has nbThreads "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nbThreads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_bcalm</span><span class="p">)</span> <span class="n" style="color: #333;">bcalm2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_storage</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">abundance</span><span class="p">,</span> <span class="n" style="color: #333;">minimizerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="n" style="color: #333;">minimizer_type</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span> </span>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_bglue</span><span class="p">)</span> <span class="n" style="color: #333;">bglue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_storage</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nb_glue_partitions</span><span class="p">,</span>       <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="idiff left right">               </span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_links</span><span class="p">)</span> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_bcalm</span><span class="p">)</span> <span class="n" style="color: #333;">bcalm2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_storage</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">abundance</span><span class="p">,</span> <span class="n" style="color: #333;">minimizerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="n" style="color: #333;">minimizer_type</span><span class="p">,</span> <span class="idiff left right">      </span><span class="n" style="color: #333;">verbose</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="116" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_bglue</span><span class="p">)</span> <span class="n" style="color: #333;">bglue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_storage</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nb_glue_partitions</span><span class="p">,</span>       <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">all_abundance_counts</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="116" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_links</span><span class="p">)</span> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">nbThreads</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">edge_km_representation</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" 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">

116

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" 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">

117

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We gather some statistics. */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" 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">

118

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<td class="diff-line-num new_line" data-linenumber="116" 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">

116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// nb_unitigs will be used in GraphUnitigs</span></span>

</pre>

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<br>

</li>

<li id="ed783240a52e80bd1c3a470d6646b3f6b3ab63e4">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4"><strong>gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1300" 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="1300" 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">@@ -1300,6 +1300,16 @@ void SortingCountAlgorithm<span>::fillPartitions (size_t pass, Iterator<Sequence</td>

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<td class="diff-line-num old_line" data-linenumber="1300" 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">

1300

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<td class="diff-line-num new_line" data-linenumber="1300" 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">

1300

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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="cpp">                         <span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1301" 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">

1301

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<td class="diff-line-num new_line" data-linenumber="1301" 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">

1301

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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1302" 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">

1302

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<td class="diff-line-num new_line" data-linenumber="1302" 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">

1302

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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1303" 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">

1303

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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1304" 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">

1304

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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// force close partitions and re-open them for reading</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1305" 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">

1305

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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// may prevent crash in large multi-bank counting instance on Lustre filesystems</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1306" 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">

1306

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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1307" 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">

1307

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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1308" 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">

1308

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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp">                 <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpStorageName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_OUTPUT_TMP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">getTemporaryFilename</span><span class="p">(</span><span class="s" style="color: #d14;">"dsk_partitions"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1309" 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="LC1309" class="line" lang="cpp">                 <span class="n" style="color: #333;">setPartitions</span>        <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// close the partitions first, otherwise new files are opened before  closing parti from previous pass</span></span>

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<td class="diff-line-num new new_line" data-linenumber="1310" 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="LC1310" class="line" lang="cpp">                 <span class="n" style="color: #333;">setPartitions</span>        <span class="p">(</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_tmpPartitionsStorage</span><span class="p">)().</span><span class="n" style="color: #333;">getPartition</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="s" style="color: #d14;">"parts"</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1311" 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">

1311

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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp">                 </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1312" 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="LC1312" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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1303

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<td class="diff-line-num new_line" data-linenumber="1313" 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">

1313

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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="cpp"> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1304" 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="LC1314" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="1305" 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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<td class="diff-line-num new_line" data-linenumber="1315" 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="LC1315" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</span></span>

</pre>

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<br>

</li>

<li id="6dc8c95d8c6c04e96a48b4cf5c3c2ea31cc93750">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#6dc8c95d8c6c04e96a48b4cf5c3c2ea31cc93750"><strong>gatb-core/src/gatb/system/impl/FileSystemCommon.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="36" 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">@@ -36,6 +36,7 @@</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/stat.h></span></span>

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<td class="diff-line-num old_line" data-linenumber="38" 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="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.h></span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>

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<td class="diff-line-num new_line" data-linenumber="42" 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="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">gatb</span>      <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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="61" 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">@@ -60,6 +61,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">    <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="61" 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="LC62" class="line" lang="cpp">        <span class="n" style="color: #333;">_isStdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span><span class="s" style="color: #d14;">"stdout"</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">        <span class="n" style="color: #333;">_handle</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_isStdout</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">stdout</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fopen</span> <span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "opening file " << _path << " handle " << _handle << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_handle</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp">           <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">                   <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span> <span class="p">(</span><span class="s" style="color: #d14;">"cannot open %s %s"</span><span class="p">,</span><span class="n" style="color: #333;">path</span><span class="p">,</span><span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">));</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,7 +69,9 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Destructor. */</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">CommonFile</span> <span class="p">()</span>  <span class="p">{</span>  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_handle</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_isStdout</span><span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">_handle</span><span class="p">);</span>  <span class="p">}</span>  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">CommonFile</span> <span class="p">()</span>  <span class="p">{</span>  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_handle</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_isStdout</span><span class="p">)</span>  <span class="p">{</span>  </span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "closing file " << _path << " handle " << _handle << std::endl; </span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">        <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">_handle</span><span class="p">);</span>  <span class="p">}</span>  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFile::isOpen */</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOpen</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getHandle</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>

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<br>

</li>

<li id="4c12716c6fcb516eda353ab99ab2b81002b77515">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#4c12716c6fcb516eda353ab99ab2b81002b77515"><strong>gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,15 +25,16 @@ template void bglue<${KSIZE}>(Storage* storage,</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">        int kmerSize, </span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">        int nb_glue_partitions, </span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">        int nb_threads, </span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">        bool all_abundance_counts,</span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">        bool verbose</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">        );</span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">template class graph3<${KSIZE}>; // graph3<span> switch  </span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">template void link_tigs<${KSIZE}></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">    (std::string unitigs_filename, int kmerSize, int nb_threads, uint64_t &nb_unitigs, bool verbose, bool renumber_unitigs = false);</span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">    (std::string unitigs_filename, int kmerSize, int nb_threads, uint64_t &nb_unitigs, bool verbose, bool <span class="idiff left right">edge_km_representation, bool </span>renumber_unitigs = false);</span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">template void link_unitigs_pass<${KSIZE}>(const std::string unitigs_filename, bool verbose, const int pass, const int kmerSize, const bool renumber_unitigs);</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="37" 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="LC37" class="line" lang="plaintext">template void link_unitigs_pass<${KSIZE}>(const std::string unitigs_filename, bool verbose, const int pass, const int kmerSize, <span class="idiff left right">bool edge_km_representation, </span>const bool renumber_unitigs);</span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">/********************************************************************************/</span>

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<br>

</li>

<li id="9be95217b1b4429f2eeabc2213c457fd389f08a0">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#9be95217b1b4429f2eeabc2213c457fd389f08a0"><strong>gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" 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="239" 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">@@ -239,6 +239,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="n" style="color: #333;">_filename</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">_filename</span><span class="p">),</span> <span class="n" style="color: #333;">_gzfile</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span>  <span class="n" style="color: #333;">_buffer</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_cpt_buffer</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_idx</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_cacheItemsNb</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">_cacheItemsNb</span><span class="p">),</span> <span class="n" style="color: #333;">_isDone</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">        <span class="n" style="color: #333;">_gzfile</span> <span class="o" style="font-weight: 600;">=</span>   <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">_filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">        <span class="n" style="color: #333;">gzbuffer</span><span class="p">(</span><span class="n" style="color: #333;">_gzfile</span><span class="p">,</span><span class="mi" style="color: #099;">2</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>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">        <span class="n" style="color: #333;">_buffer</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MALLOC</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_cacheItemsNb</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" 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="249" 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">@@ -248,6 +249,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">        <span class="n" style="color: #333;">_gzfile</span> <span class="o" style="font-weight: 600;">=</span>   <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">_filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="251" 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="LC252" class="line" lang="cpp">        <span class="n" style="color: #333;">gzbuffer</span><span class="p">(</span><span class="n" style="color: #333;">_gzfile</span><span class="p">,</span><span class="mi" style="color: #099;">2</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>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">        <span class="n" style="color: #333;">_buffer</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MALLOC</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_cacheItemsNb</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="254" 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="LC254" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="273" 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="275" 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">@@ -273,6 +275,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp">            <span class="n" style="color: #333;">_isDone</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">_isDone</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp">            </span>

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<td class="diff-line-num old_line" data-linenumber="275" 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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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp">            <span class="n" style="color: #333;">_gzfile</span> <span class="o" style="font-weight: 600;">=</span>   <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">_filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="278" 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="LC278" class="line" lang="cpp">            <span class="n" style="color: #333;">gzbuffer</span><span class="p">(</span><span class="n" style="color: #333;">_gzfile</span><span class="p">,</span><span class="mi" style="color: #099;">2</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>

</pre>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp">            <span class="n" style="color: #333;">_buffer</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MALLOC</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Item</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">_cacheItemsNb</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

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<br>

</li>

<li id="4ae6c527aafe52f4f16907962f525902d4b5ef6f">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#4ae6c527aafe52f4f16907962f525902d4b5ef6f"><strong>gatb-core/src/gatb/tools/misc/api/StringsRepository.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,6 +83,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">graph</span>          <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-graph"</span><span class="p">;</span>          <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmer_size</span>      <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-kmer-size"</span><span class="p">;</span>      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">minimizer_size</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-minimizer-size"</span><span class="p">;</span> <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">edge_km_representation</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-edge-km"</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">all_abundance_counts</span>   <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-all-abundance-counts"</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmer_abundance</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-abundance"</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmer_abundance_min</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-abundance-min"</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kmer_abundance_min_threshold</span> <span class="p">()</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"-abundance-min-threshold"</span><span class="p">;</span> <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" 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="140" 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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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_URI_GRAPH           gatb::core::tools::misc::StringRepository::singleton().graph ()</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_KMER_SIZE           gatb::core::tools::misc::StringRepository::singleton().kmer_size ()</span></span>

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<td class="diff-line-num new_line" data-linenumber="142" 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="LC142" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_MINIMIZER_SIZE      gatb::core::tools::misc::StringRepository::singleton().minimizer_size ()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_EDGE_KM_REPRESENTATION      gatb::core::tools::misc::StringRepository::singleton().edge_km_representation ()</span></span>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_ALL_ABUNDANCE_COUNTS        gatb::core::tools::misc::StringRepository::singleton().all_abundance_counts ()</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_INTEGER_PRECISION   gatb::core::tools::misc::StringRepository::singleton().integer_precision ()</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_KMER_ABUNDANCE      gatb::core::tools::misc::StringRepository::singleton().kmer_abundance ()</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define STR_KMER_ABUNDANCE_MIN  gatb::core::tools::misc::StringRepository::singleton().kmer_abundance_min ()</span></span>

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<li id="3b8fda1a420e311e4fb4b0d9fe344d4bbc2f4e97">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#3b8fda1a420e311e4fb4b0d9fe344d4bbc2f4e97"><strong>gatb-core/src/gatb/tools/misc/impl/Tool.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="57" 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">@@ -57,7 +57,6 @@ Tool::Tool (const std::string& name) : userDisplayHelp(0), _helpTarget(0),userDi</td>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">,</span>    <span class="s" style="color: #d14;">"number of cores"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span>  <span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">    <span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_VERBOSE</span><span class="p">,</span>     <span class="s" style="color: #d14;">"verbosity level"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span>  <span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp">   </span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">   <span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_VERSION</span><span class="p">,</span> <span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">   <span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_HELP</span><span class="p">,</span> <span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"></span>

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<li id="f84f48b86f89b6fe6f3b401f6ed674d1ffab829b">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#f84f48b86f89b6fe6f3b401f6ed674d1ffab829b"><strong>gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="266" 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">@@ -266,6 +266,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">        <span class="n" style="color: #333;">herr_t</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "begin insert" << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp">            <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LocalSynchronizer</span> <span class="n" style="color: #333;">localsynchro</span> <span class="p">(</span><span class="n" style="color: #333;">_common</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_synchro</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** We get the dataset id. */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="300" 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">@@ -300,6 +301,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Sclose</span> <span class="p">(</span><span class="n" style="color: #333;">filespaceId</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Sclose</span> <span class="p">(</span><span class="n" style="color: #333;">memspaceId</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"err H5Sclose"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "end insert" << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We periodically clean up some HDF5 resources. */</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="375" 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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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         * NOTE !!!  the 'clean' method called after this block is also synchronized,</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">         * and therefore must not be in the same instruction block. */</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "begin retrievecache" << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp">            <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LocalSynchronizer</span> <span class="n" style="color: #333;">localsynchro</span> <span class="p">(</span><span class="n" style="color: #333;">_common</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_synchro</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp">            <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">memspaceId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Screate_simple</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** Select hyperslab on file dataset. */</span></span>

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<td class="diff-line-num old_line" data-linenumber="381" 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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<td class="diff-line-num new_line" data-linenumber="384" 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="LC384" class="line" lang="cpp">            <span class="n" style="color: #333;">hid_t</span> <span class="n" style="color: #333;">filespaceId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Dget_space</span><span class="p">(</span><span class="n" style="color: #333;">_common</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDatasetId</span><span class="p">());</span></span>

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<td class="diff-line-num new old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="385" 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="LC385" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "filespaceId "  << filespaceId << std::endl;</span></span>

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382

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<td class="diff-line-num new_line" data-linenumber="386" 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="LC386" class="line" lang="cpp">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Sselect_hyperslab</span> <span class="p">(</span><span class="n" style="color: #333;">filespaceId</span><span class="p">,</span> <span class="n" style="color: #333;">H5S_SELECT_SET</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="383" 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">

383

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<td class="diff-line-num new_line" data-linenumber="387" 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">

387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">gatb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exception</span> <span class="p">(</span><span class="s" style="color: #d14;">"HDF5 error (H5Sselect_hyperslab), status %d"</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">);</span>  <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -390,6 +394,7 @@ private:</td>

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<td class="diff-line-num new_line" data-linenumber="394" 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">

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Sclose</span> <span class="p">(</span><span class="n" style="color: #333;">filespaceId</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" 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">

391

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<td class="diff-line-num new_line" data-linenumber="395" 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">

395

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Sclose</span> <span class="p">(</span><span class="n" style="color: #333;">memspaceId</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="392" 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">

392

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<td class="diff-line-num new_line" data-linenumber="396" 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">

396

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">gatb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exception</span> <span class="p">(</span><span class="s" style="color: #d14;">"HDF5 error (H5Sclose), status %d"</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">);</span>  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="397" 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="LC397" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "end retrievecache" << std::endl;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="398" 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">

398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="399" 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">

399

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="395" 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="LC400" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We periodically clean up some HDF5 resources. */</span></span>

</pre>

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<br>

</li>

<li id="9e0109d139212f56eef6153e59e64fa4c6670360">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#9e0109d139212f56eef6153e59e64fa4c6670360"><strong>gatb-core/src/gatb/tools/storage/impl/Storage.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="181" 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="181" 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">@@ -181,7 +181,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" 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="LC182" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Get a child partition from its name. Created if not already exists.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] name : name of the child partition to be retrieved.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] nb : in case of creation, tells how many collection belong to the partition.</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] nb : in case of creation, tells how many collection belong to the partition.<span class="idiff left right"> IMPORTANT: if nb != 0, StorageFile will erase the partition before opening it. So if you're opening a partition, just set nb=0 and let it autodetect the size</span></span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \return the child partition.</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Type</span><span class="o" style="font-weight: 600;">></span>  <span class="n" style="color: #333;">Partition</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">getPartition</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nb</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<br>

</li>

<li id="efdf123a4ecf95f1a9326ff6d3443694ceed944f">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#efdf123a4ecf95f1a9326ff6d3443694ceed944f"><strong>gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="96" 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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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">GroupFile</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp">                           <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// hack to remove the trashme folers. I'd have liked to make that call in remove() but for some reason remove() isn't called</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout << "groupfile destructor called, removing folder " << folder << std::endl;</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">                <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// hack to remove the trashme folers. I'd have liked to make that call in remove() but for some reason remove() isn't called</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="220" 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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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">isFolderEndingWith</span><span class="p">(</span><span class="n" style="color: #333;">storage_prefix</span><span class="p">,</span><span class="s" style="color: #d14;">"_gatb"</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">            <span class="n" style="color: #333;">file_folder</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"_gatb/"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_folder</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFullId</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">getDirectory</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">getBaseName</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// because gatb's getBaseName is stupid and cuts after the last dot</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">full_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_folder</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" 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="LC224" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">parent_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFullId</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">base_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent_base</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="226" 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="LC226" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parent_base</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="227" 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="LC227" class="line" lang="cpp">            <span class="n" style="color: #333;">base_name</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// because gatb's getBaseName is stupid and cuts after the last dot</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="228" 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="LC228" class="line" lang="cpp">        <span class="n" style="color: #333;">base_name</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">name</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="229" 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="LC229" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="230" 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="LC230" class="line" lang="cpp">        <span class="n" style="color: #333;">full_path</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">base_name</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// but then base_name might have a suffix like ".1" for partitions</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="231" 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="LC231" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="232" 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="LC232" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout <<"name: " << name << " filename " << full_path << " prefix " << base_name<< std::endl;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">        <span class="p">{</span>   <span class="c1" style="color: #998; font-style: italic;">// if nb is 0, it means we're opening partitions and not creating them, thus we need to get the number of partitions.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_partitions</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp">           <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;">filename</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">           <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;">filename</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_f</span>older</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">            <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">prefix</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prefix</span></span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">// startswith</span></span>

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<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="240" 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="LC240" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">base_name</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">base_name</span></span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">// startswith</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">                <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp">                    <span class="n" style="color: #333;">nb_partitions</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">                <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="240" 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="248" 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">@@ -240,19 +248,20 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error: could not get number of partition for "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" using StorageFile"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">                <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="250" 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="LC250" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "got " << nb << " partitions" << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="244" 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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<td class="diff-line-num new_line" data-linenumber="253" 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="LC253" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="245" 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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<td class="diff-line-num new_line" data-linenumber="254" 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="LC254" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="246" 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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<td class="diff-line-num new_line" data-linenumber="255" 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="LC255" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// else, if nb is set, means we're creating some partitions. let's delete all the previous ones to avoid wrongly counting </span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp">            <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;">filename</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="256" 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="LC256" class="line" lang="cpp">            <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;">filename</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_f</span>older</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="257" 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="LC257" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout <<"name: " << name << " comparing " << filename << " with prefix " << <span class="idiff left right">prefix</span> << std::endl;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">prefix</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prefix</span></span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">// startswith</span></span>

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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="258" 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="LC258" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout <<"name: " << name << " comparing " << filename << " with prefix " << <span class="idiff left right">base_name</span> << std::endl;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">base_name</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">base_name</span></span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">// startswith</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" 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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<td class="diff-line-num new_line" data-linenumber="260" 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="LC260" class="line" lang="cpp">                <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="252" 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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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">// some additional guard:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="253" 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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<td class="diff-line-num new_line" data-linenumber="262" 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="LC262" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span> <span class="o" style="font-weight: 600;">||</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".."</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp">                    <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">folder</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">//std::cout << "deleting<span class="idiff left right">" << </span>folder << "/" << filename << std::endl;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">                    <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_f</span>older</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">//std::cout << "deleting<span class="idiff left right"> " << file_</span>folder << "/" << filename << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp">        <span class="p">}</span></span>

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<li id="dd31cf0d08329fcf5ce3e2647df00c99baa267ba">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#dd31cf0d08329fcf5ce3e2647df00c99baa267ba"><strong>gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" 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="268" 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">@@ -268,6 +268,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">actualName</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFullId</span><span class="p">(</span><span class="sc" style="color: #d14;">'/'</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp">                <span class="cm" style="color: #998; font-style: italic;">/** We create the HDF5 group if needed. */</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//std::cout << "actualname: "<< actualName << " end"<<std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp">                <span class="n" style="color: #333;">htri_t</span> <span class="n" style="color: #333;">doesExist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H5Lexists</span> <span class="p">(</span><span class="n" style="color: #333;">storage</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFileId</span><span class="p">(),</span> <span class="n" style="color: #333;">actualName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">H5P_DEFAULT</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doesExist</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<li id="d7401b2bb5a2b6245ce8cd38b4b1c20e7ea1a058">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#d7401b2bb5a2b6245ce8cd38b4b1c20e7ea1a058"><strong>gatb-core/test/unit/src/debruijn/TestDebruijn.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="87" 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">@@ -87,6 +87,7 @@ class TestDebruijn : public Test</td>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="n" style="color: #333;">CPPUNIT_TEST_SUITE_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">TestDebruijn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" 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="LC89" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="90" 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="LC90" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_build</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="91" 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="LC91" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_test_small_kmers</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" 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="LC92" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_large_abundance_query</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" 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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<td class="diff-line-num new_line" data-linenumber="93" 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="LC93" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_test7</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,7 +105,6 @@ class TestDebruijn : public Test</td>

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<td class="diff-line-num old_line" data-linenumber="104" 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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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_test12</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_test13</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//        CPPUNIT_TEST_GATB (debruijn_mutation); // has been removed due to it crashing clang, and since mutate() isn't really used in apps, i didn't bother.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_build</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" 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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<td class="diff-line-num new_line" data-linenumber="108" 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="LC108" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_checkbranching</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_mphf</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" 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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<td class="diff-line-num new_line" data-linenumber="110" 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">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">debruijn_mphf_nodeindex</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="908" 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="908" 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">@@ -908,13 +908,22 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="908" 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">

908

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<td class="diff-line-num new_line" data-linenumber="908" 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">

908

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<pre style="margin: 0;"> <span id="LC908" class="line" lang="cpp">        <span class="n" style="color: #333;">IBank</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inputBank</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankStrings</span> <span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">nbSequences</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="909" 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">

909

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<td class="diff-line-num new_line" data-linenumber="909" 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">

909

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<pre style="margin: 0;"> <span id="LC909" class="line" lang="cpp">        <span class="n" style="color: #333;">LOCAL</span> <span class="p">(</span><span class="n" style="color: #333;">inputBank</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="910" 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">

910

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<td class="diff-line-num new_line" data-linenumber="910" 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">

910

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<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="911" 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">

911

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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="912" 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">

912

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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "g1 create" << std::endl;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="911" 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">

911

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<td class="diff-line-num new_line" data-linenumber="913" 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">

913

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<pre style="margin: 0;"> <span id="LC913" class="line" lang="cpp">        <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">create</span> <span class="p">(</span><span class="n" style="color: #333;">inputBank</span><span class="p">,</span>  <span class="s" style="color: #d14;">"-kmer-size 31 -out %s -abundance-min 1  -verbose 0  -max-memory %d"</span><span class="p">,</span>                        <span class="s" style="color: #d14;">"g1"</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_MEMORY</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="914" 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">

914

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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="912" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="915" 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">

915

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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "g2 create" << std::endl;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="912" 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">

912

</td>

<td class="diff-line-num new_line" data-linenumber="916" 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">

916

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<pre style="margin: 0;"> <span id="LC916" class="line" lang="cpp">        <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">create</span> <span class="p">(</span><span class="n" style="color: #333;">inputBank</span><span class="p">,</span>  <span class="s" style="color: #d14;">"-kmer-size 31 -out %s -abundance-min 1  -verbose 0 -branching-nodes none  -max-memory %d"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"g2"</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

913

</td>

<td class="diff-line-num new_line old" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC913" class="line" lang="cpp">        <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">create</span> <span class="p">(</span><span class="n" style="color: #333;">inputBank</span><span class="p">,</span>  <span class="s" style="color: #d14;">"-kmer-size 31 -out %s -abundance-min 1  -verbose 0 -solid-kmers-out none  -max-memory %d"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"g3"</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_MEMORY</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="917" 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">

917

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="918" 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">

918

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC918" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// This test doesn't work anymore.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="919" 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">

919

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// It's probably a small fix somewehre</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="920" 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">

920

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// But I'd argue that the gatb feature of 'not outputting solid kmers to disk' is useless</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="921" 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">

921

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// So instead of bothering, I'm just removing the present unit test.</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="914" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="922" 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">

922

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//Graph::create (inputBank,  "-kmer-size 31 -out %s -abundance-min 1  -verbose 0 -solid-kmers-out none -debloom none -branching-nodes none -max-memory %d",  "g3", MAX_MEMORY);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="914" 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">

914

</td>

<td class="diff-line-num new_line" data-linenumber="923" 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">

923

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="915" 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">

915

</td>

<td class="diff-line-num new_line" data-linenumber="924" 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">

924

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC924" class="line" lang="cpp">        <span class="n" style="color: #333;">debruijn_build_entry</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">debruijn_build_aux_aux</span> <span class="p">(</span><span class="s" style="color: #d14;">"g1"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="916" 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">

916

</td>

<td class="diff-line-num new_line" data-linenumber="925" 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">

925

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp">        <span class="n" style="color: #333;">debruijn_build_entry</span> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">debruijn_build_aux_aux</span> <span class="p">(</span><span class="s" style="color: #d14;">"g2"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

917

</td>

<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC917" class="line" lang="cpp">        <span class="n" style="color: #333;">debruijn_build_entry</span> <span class="n" style="color: #333;">r3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">debruijn_build_aux_aux</span> <span class="p">(</span><span class="s" style="color: #d14;">"g3"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="918" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="926" 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">

926

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>debruijn_build_entry r3 = debruijn_build_aux_aux ("g3", false, true);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="918" 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">

918

</td>

<td class="diff-line-num new_line" data-linenumber="927" 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">

927

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="919" 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">

919

</td>

<td class="diff-line-num new_line" data-linenumber="928" 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">

928

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">nbNodes</span>       <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">nbNodes</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="920" 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">

920

</td>

<td class="diff-line-num new_line" data-linenumber="929" 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">

929

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">checksumNodes</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">checksumNodes</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="925" 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="934" 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">@@ -925,8 +934,8 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="925" 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">

925

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<td class="diff-line-num new_line" data-linenumber="934" 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">

934

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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="926" 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">

926

</td>

<td class="diff-line-num new_line" data-linenumber="935" 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">

935

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<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">nbBranchingNodes</span>       <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">nbBranchingNodes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="927" 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">

927

</td>

<td class="diff-line-num new_line" data-linenumber="936" 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">

936

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<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">checksumBranchingNodes</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">checksumBranchingNodes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

928

</td>

<td class="diff-line-num new_line old" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC928" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left">CPPUNIT_ASSERT</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nbBranchingNodes</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">r3</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nbBranchingNodes</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

929

</td>

<td class="diff-line-num new_line old" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC929" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">checksumBranchingNodes</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r3</span><span class="p">.</span><span class="n" style="color: #333;">checksumBranchingNodes</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="930" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="937" 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">

937

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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//CPPUNIT_ASSERT (r1.nbBranchingNodes       == r3.nbBranchingNodes); // uncomment if we ever fix r3 (see long comment above)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="930" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="938" 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">

938

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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>CPPUNIT_ASSERT (r1.checksumBranchingNodes == r3.checksumBranchingNodes);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="930" 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">

930

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<td class="diff-line-num new_line" data-linenumber="939" 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">

939

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<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="931" 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">

931

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<td class="diff-line-num new_line" data-linenumber="940" 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">

940

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<pre style="margin: 0;"> <span id="LC940" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="932" 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">

932

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<td class="diff-line-num new_line" data-linenumber="941" 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">

941

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<pre style="margin: 0;"> <span id="LC941" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>

</pre>

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<br>

</li>

<li id="49ce0c04f76f93b18c25528d056dc803569026e0">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#49ce0c04f76f93b18c25528d056dc803569026e0"><strong>gatb-core/test/unit/src/kmer/TestDSK.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="471" 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="471" 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">@@ -471,6 +471,9 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="471" 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">

471

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<td class="diff-line-num new_line" data-linenumber="471" 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">

471

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// printf ("min=%ld  max=%ld  nb=%ld  check=%ld \n",</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="472" 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">

472

</td>

<td class="diff-line-num new_line" data-linenumber="472" 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">

472

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//    nksMin, nksMax, sortingCount.getSolidCounts()->getNbItems(),checkNb</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="473" 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">

473

</td>

<td class="diff-line-num new_line" data-linenumber="473" 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">

473

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// );</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="474" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="474" 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">

474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="474" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="475" 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">

475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sortingCount</span><span class="p">.</span><span class="n" style="color: #333;">getSolidCounts</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbItems</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">checkNb</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="474" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="476" 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">

476

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"counted "</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">sortingCount</span><span class="p">.</span><span class="n" style="color: #333;">getSolidCounts</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbItems</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" kmers, expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">checkNb</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp">        <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">sortingCount</span><span class="p">.</span><span class="n" style="color: #333;">getSolidCounts</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbItems</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">checkNb</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp">    <span class="p">}</span></span>

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<li id="e2e4e0dc5c61805b798db5e2dee529b92e327235">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#e2e4e0dc5c61805b798db5e2dee529b92e327235"><strong>gatb-core/test/unit/src/tools/storage/TestStorage.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nbIter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp">            <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NativeInt64</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">iterator</span><span class="p">();</span>    <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">(),</span> <span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">);</span>  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">(),</span> <span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>  <span class="p">{</span>  </span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"item "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" expected: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span>            </span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp">                <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">);</span>  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">            <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">nbIter</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="LC140" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,7 +155,9 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">            <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NativeInt64</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partition</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">iterator</span><span class="p">();</span>    <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">(),</span> <span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span>  <span class="p">);</span> <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="cpp">                                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"item "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" expected: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span>            </span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">                      <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span>  <span class="p">);</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nbIter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">            <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">nbIter</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

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<br>

</li>

<li id="e79cab2022b11c71b2d8095f0ebe49260b3cc139">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/d6238780168fff561ee805fa30923f988a8b9a3e#e79cab2022b11c71b2d8095f0ebe49260b3cc139"><strong>gatb-core/thirdparty/update-boost.sh</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#this is the procedure I use to update to newer versions of boost in gatb-core</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#pretty simple but gets the job done</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#to be run within thirdparty/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-Rayan</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">newdir</span><span class="o" style="font-weight: 600;">=</span>boost_1_71_0/boost/</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">olddir</span><span class="o" style="font-weight: 600;">=</span>boost</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>file <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$olddir</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-R</span> <span class="nv" style="color: #008080;">$newdir</span>/<span class="nv" style="color: #008080;">$file</span> <span class="nv" style="color: #008080;">$olddir</span>/</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>

</td>

</tr>

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