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<h3>
Andreas Tille 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/8e45a9a10a24b387c839913a974e40f9dff2c517">8e45a9a1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-14T21:36:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.1+dfsg</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4c007bda60857aed5186f73b4dd88ee753952d0d">
gatb-core/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#635176faaab64014f3c4f1f69d72a59733222221">
gatb-core/RELEASES.md
</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="#13ea1c05cb7d9ae8ed463fc61e80763d1ced17a4">
gatb-core/src/gatb/bcalm2/ograph.cpp
</a>
</li>
<li class="file-stats">
<a href="#e5f4aedaa4ba7e44690deaee2cca509fc116878c">
gatb-core/src/gatb/bcalm2/unionFind.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="#9b5b9f4932f76dfc0009ce5285cfa8f0f23f4e08">
gatb-core/src/gatb/tools/collections/impl/Bloom.hpp
</a>
</li>
<li class="file-stats">
<a href="#d20a6d3ee161043e501a14dd28c584ee3f648451">
gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp
</a>
</li>
<li class="file-stats">
<a href="#f277743fafad21b1db3cfefe81a886858b79c0d2">
gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp
</a>
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<li class="file-stats">
<a href="#9c52420fe937907fda5e3bd167986dd5f6434d76">
gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp
</a>
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<li class="file-stats">
<a href="#ebaa2f2e74863bc0d1c5240d9ff0ce14b78c270d">
gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp
</a>
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<li class="file-stats">
<a href="#efdf123a4ecf95f1a9326ff6d3443694ceed944f">
gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp
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<li class="file-stats">
<a href="#318096db5deb1f35e51713c65641cded76fcd620">
gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp
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<li class="file-stats">
<a href="#28fbddbc4a2511be4726a07641fb02a01e5d97b7">
<span class="deleted-file">
−
gatb-core/test/db/NIST7035_TAAGGCGA_L001_R1_001_5OK.fastq.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#60989b7babc1e5766eb2e081e6790c643a0ad4ef">
<span class="deleted-file">
−
gatb-core/test/db/NIST7035_TAAGGCGA_L001_R1_001_5OK.fastq.leon-ref
</span>
</a>
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<li class="file-stats">
<a href="#92e06bf6e5b5bd0c3ac5d6e283340ef6ac34dbaa">
<span class="deleted-file">
−
gatb-core/test/db/giab.hg002.2D_6K.fastq.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#e55d7d0a8f1913c2616eb501673647e62a51aae6">
gatb-core/test/unit/src/bank/TestLeon.cpp
</a>
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<li class="file-stats">
<a href="#fcfa76d64a82d58d9a219299e6272ce3d8768f9c">
<span class="new-file">
+
gatb-core/test/unit/src/bcalm/TestBcalm.cpp
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4c007bda60857aed5186f73b4dd88ee753952d0d">
<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#4c007bda60857aed5186f73b4dd88ee753952d0d"><strong>gatb-core/CMakeLists.txt</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 3.1.0)</td>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The default version number is the latest official build</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_MAJOR 1<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_MINOR 4<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_PATCH <span class="idiff left right">0</span><span class="p">)</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-core_VERSION_PATCH <span class="idiff left right">1</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(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="LC14" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># But, it is possible to define another release number during a local build</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
</pre>
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<br>
</li>
<li id="635176faaab64014f3c4f1f69d72a59733222221">
<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#635176faaab64014f3c4f1f69d72a59733222221"><strong>gatb-core/RELEASES.md</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gh" style="color: #999;"># RELEASE 1.4.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="markdown"></span>
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<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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">*</span> This is a bugfix release</span>
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<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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p"> *</span> fixed a segfault in some multi-threaded situations</span>
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<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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p"> *</span> removed some spurious large files in the distrib</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"> *</span> fixed a bug with the -storate-type file option</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gh" style="color: #999;"># RELEASE 1.4.0</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">*</span> Integration of Leon compressor into GATB-Core :</span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#490f86cdfc07e7db3455fffd8859052bd5dbeb50"><strong>gatb-core/src/gatb/bcalm2/bglue_algo.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -791,7 +791,10 @@ void bglue(Storage *storage,</td>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">ModelCanon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span> <span class="n" style="color: #333;">kmmerBegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelCanon</span><span class="p">.</span><span class="n" style="color: #333;">codeSeed</span><span class="p">(</span><span class="n" style="color: #333;">kmerBegin</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">Data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ASCII</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">ModelCanon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span> <span class="n" style="color: #333;">kmmerEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelCanon</span><span class="p">.</span><span class="n" style="color: #333;">codeSeed</span><span class="p">(</span><span class="n" style="color: #333;">kmerEnd</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">Data</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ASCII</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">ufkmers</span><span class="p">.</span><span class="n" style="color: #333;">union_</span><span class="p">(</span><span class="n" style="color: #333;">uf_mphf</span><span class="p">.</span><span class="n" style="color: #333;">lookup</span><span class="p">(</span><span class="n" style="color: #333;">hasher</span><span class="p">(</span><span class="n" style="color: #333;">kmmerBegin</span><span class="p">)),</span> <span class="n" style="color: #333;">uf_mphf</span><span class="p">.</span><span class="n" style="color: #333;">lookup</span><span class="p">(</span><span class="n" style="color: #333;">hasher</span><span class="p">(</span><span class="n" style="color: #333;">kmmerEnd</span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf_mphf</span><span class="p">.</span><span class="n" style="color: #333;">lookup</span><span class="p">(</span><span class="n" style="color: #333;">hasher</span><span class="p">(</span><span class="n" style="color: #333;">kmmerBegin</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf_mphf</span><span class="p">.</span><span class="n" style="color: #333;">lookup</span><span class="p">(</span><span class="n" style="color: #333;">hasher</span><span class="p">(</span><span class="n" style="color: #333;">kmmerEnd</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;">ufkmers</span><span class="p">.</span><span class="n" style="color: #333;">union_</span><span class="p">(</span><span class="n" style="color: #333;">v1</span><span class="p">,</span><span class="n" style="color: #333;">v2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ufkmers.union_((hasher(kmmerBegin)), (hasher(kmmerEnd)));</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</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">@@ -818,10 +821,9 @@ void bglue(Storage *storage,</td>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//setDispatcher (new SerialDispatcher()); // force single thread</span></span>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">Dispatcher</span> <span class="n" style="color: #333;">dispatcher</span> <span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">dispatcher</span><span class="p">.</span><span class="n" style="color: #333;">iterate</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iterator</span><span class="p">(),</span> <span class="n" style="color: #333;">createUF</span><span class="p">);</span></span>
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824
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="cpp"></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> </span>
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825
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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826
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> ufmin.printStats("uf minimizers");</span></span>
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827
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="836" style="width: 35px; color: rgba(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="838" style="width: 35px; color: rgba(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">@@ -836,6 +838,7 @@ void bglue(Storage *storage,</td>
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836
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_uf_stats</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// for debugging</span></span>
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837
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="cpp"> <span class="p">{</span></span>
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838
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">ufkmers</span><span class="p">.</span><span class="n" style="color: #333;">printStats</span><span class="p">(</span><span class="s" style="color: #d14;">"uf kmers"</span><span class="p">);</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ufkmers.dumpUF("uf.dump");</span></span>
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839
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"after computing UF stats"</span><span class="p">);</span></span>
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840
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="cpp"> <span class="p">}</span></span>
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841
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -929,6 +932,7 @@ void bglue(Storage *storage,</td>
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929
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"></span>
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930
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="cpp"> <span class="n" style="color: #333;">logging</span><span class="p">(</span> <span class="s" style="color: #d14;">"Allowed "</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;">max_buffer</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nbGluePartitions</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 memory for buffers"</span><span class="p">);</span></span>
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931
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp"></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"></span>
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932
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// partition the glue into many files, à la dsk</span></span>
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933
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937
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<pre style="margin: 0;"> <span id="LC937" 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>
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934
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938
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<pre style="margin: 0;"> <span id="LC938" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="983" style="width: 35px; color: rgba(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="987" style="width: 35px; color: rgba(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">@@ -983,7 +987,7 @@ void bglue(Storage *storage,</td>
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983
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">gluePartitions</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// takes care of the final flush (this doesn't delete the file, just closes it)</span></span>
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">gluePartitions</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"Done disk partitioning of glue"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC993" 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">@@ -1010,10 +1014,11 @@ void bglue(Storage *storage,</td>
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// glue all partitions using a thread pool</span></span>
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadPool</span> <span class="n" style="color: #333;">pool</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1017" 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;">mutex</span> <span class="n" style="color: #333;">mtx</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// lock to avoid a nasty bug when calling output()</span></span>
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1018
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<pre style="margin: 0;"> <span id="LC1018" 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>
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="cpp"> <span class="p">{</span></span>
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1015
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1020
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<pre style="margin: 0;"> <span id="LC1020" 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>
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<pre style="margin: 0;">-<span id="LC1016" 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out_id</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>
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<pre style="margin: 0;">+<span id="LC1021" 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out_id</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="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">mtx</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>
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"> <span class="p">{</span></span>
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1023
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<pre style="margin: 0;"> <span id="LC1023" 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>
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1024
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<pre style="margin: 0;"> <span id="LC1024" 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">@@ -1101,7 +1106,12 @@ void bglue(Storage *storage,</td>
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1107" 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>
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1103
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<pre style="margin: 0;"> <span id="LC1108" 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>
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<pre style="margin: 0;">-<span id="LC1104" 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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">out_id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</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</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>
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"> <span class="p">{</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// for some reason i do need that lock_guard here.. even though output is itself lock guarded. maybe some lazyness in the evauation of the to_string(out_id++)? who kon</span></span>
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// anyway this fixes the problem, i'll understand it some other time.</span></span>
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<pre style="margin: 0;">+<span id="LC1112" 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;">lock_guard</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;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">mtx</span><span class="p">);</span></span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" 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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">out_id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</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</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>
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="p">}</span></span>
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp"> <span class="p">}</span></span>
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">ordered_sequences_idxs</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">@@ -126,7 +126,7 @@ template<size_t span></td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">graph3</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;">compaction</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iL</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iR</span><span class="p">,</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">graph3</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;">kmerType</span> <span class="n" style="color: #333;">kmmer</span><span class="p">){</span></span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">iR</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">iL</span><span class="p">){</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">graph3</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;">kmerType</span> <span class="n" style="color: #333;">RC</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rcb</span><span class="p">(</span><span class="n" style="color: #333;">kmmer</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">s1</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()),</span><span class="n" style="color: #333;">s2</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>uint s1(unitigs[iL].size()),s2(unitigs[iR].size());</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">b1</span><span class="p">(</span><span class="n" style="color: #333;">isNumber</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])),</span><span class="n" style="color: #333;">b2</span><span class="p">(</span><span class="n" style="color: #333;">isNumber</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">b1</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">b2</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">compaction</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">]),</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">]),</span><span class="n" style="color: #333;">kmmer</span><span class="p">);}</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">compaction</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">]),</span><span class="n" style="color: #333;">iR</span><span class="p">,</span><span class="n" style="color: #333;">kmmer</span><span class="p">);}</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#e5f4aedaa4ba7e44690deaee2cca509fc116878c"><strong>gatb-core/src/gatb/bcalm2/unionFind.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,7 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <set></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <atomic></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_map></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -130,6 +131,15 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC131" 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;">"raw space of UF hash data: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">getNumKeys</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;">T</span><span class="p">)</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" MB"</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="c1" style="color: #998; font-style: italic;">// 2x because each key of type T is associated to a value of type T</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// debug function</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">dumpUF</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;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">dumpfile</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;">dumpfile</span><span class="p">.</span><span class="n" style="color: #333;">open</span> <span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC139" 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;">uint32_t</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">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;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpfile</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mData</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;">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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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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134
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">mutable</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">atomic</span><span class="o" style="font-weight: 600;"><</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;">mData</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#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="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -309,7 +309,6 @@ void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span</td>
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309
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>
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310
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"builGraph for bank '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bank</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getId</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'"</span></span>
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" kmerSize="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">kmerSize</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" nksMin="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nksMin</span></span>
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313
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" output='"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'"</span></span>
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314
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#9b5b9f4932f76dfc0009ce5285cfa8f0f23f4e08"><strong>gatb-core/src/gatb/tools/collections/impl/Bloom.hpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1277" style="width: 35px; color: rgba(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">@@ -1277,6 +1277,7 @@ public:</td>
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1277
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kmerSizeStr</span></span>
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1278
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">)</span></span>
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1279
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "custom createbloom, name=" << name << " size=" << sizeStr << " nbHash=" << nbHashStr << " k=" << kmerSizeStr << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BloomKind</span> <span class="n" style="color: #333;">kind</span><span class="p">;</span> <span class="n" style="color: #333;">parse</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">kind</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">createBloom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">kind</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">)</span><span class="n" style="color: #333;">atol</span> <span class="p">(</span><span class="n" style="color: #333;">sizeStr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">atol</span> <span class="p">(</span><span class="n" style="color: #333;">nbHashStr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="n" style="color: #333;">atol</span> <span class="p">(</span><span class="n" style="color: #333;">kmerSizeStr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#d20a6d3ee161043e501a14dd28c584ee3f648451"><strong>gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,7 +113,9 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">flush</span> <span class="p">()</span> <span class="p">{</span> <span class="n" style="color: #333;">_bag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc Collection::addProperty */</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addProperty</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;">key</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;">value</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addProperty</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;">key</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;">value</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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;">"warning: collectionAbstract.addProperty() called without an implementation (notify a developer)"</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="LC118" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc Collection::addProperty */</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addProperty</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;">key</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">format</span> <span class="p">...)</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#f277743fafad21b1db3cfefe81a886858b79c0d2"><strong>gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,6 +41,7 @@ namespace gatb { namespace core { namespace tools { namespace misc { namespac</td>
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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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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TimeInfo</span> <span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_time</span><span class="p">(</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;">time</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</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="kr" style="font-weight: 600;">thread</span><span class="p">().</span><span class="n" style="color: #333;">newSynchronizer</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</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">@@ -53,6 +54,7 @@ TimeInfo::TimeInfo () : _time(system::impl::System::time())</td>
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53
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54
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<pre style="margin: 0;"> <span id="LC54" 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="LC55" class="line" lang="cpp"><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TimeInfo</span> <span class="p">(</span><span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ITime</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aTime</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_time</span><span class="p">(</span><span class="n" style="color: #333;">aTime</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;">_synchro</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="kr" style="font-weight: 600;">thread</span><span class="p">().</span><span class="n" style="color: #333;">newSynchronizer</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</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">@@ -68,6 +70,16 @@ void TimeInfo::start (const char* name)</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">_entriesT0</span> <span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_time</span><span class="p">.</span><span class="n" style="color: #333;">getTimeStamp</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//destructor</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">TimeInfo</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_synchro</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">_synchro</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</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="LC81" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC83" 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="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** METHOD :</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** PURPOSE :</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">@@ -87,17 +99,21 @@ void TimeInfo::stop (const char* name)</td>
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87
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** INPUT :</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** OUTPUT :</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** RETURN :</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** REMARKS :</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ** REMARKS :</span></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;"> GR: this must be thread safe ! because multiple threads may call this on the same TimeInfo object at the same time !</span></span>
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<pre style="margin: 0;"> <span id="LC104" 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="LC105" class="line" lang="cpp"><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ti</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">.</span><span class="n" style="color: #333;">getEntries</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lock</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">map</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="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">.</span><span class="n" style="color: #333;">getEntries</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="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entries</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">ti</span><span class="p">.</span><span class="n" style="color: #333;">getEntries</span><span class="p">().</span><span class="n" style="color: #333;">end</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>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">_entries</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;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC117" 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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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"><span class="p">}</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,14 +124,18 @@ TimeInfo& TimeInfo::operator+= (TimeInfo& ti)</td>
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108
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** OUTPUT :</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** RETURN :</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">** REMARKS :</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GR: this must be thread safe ! because multiple threads may call this on the same TimeInfo object at the same time !</span></span>
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<pre style="margin: 0;"> <span id="LC128" 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="LC129" class="line" lang="cpp"><span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">TimeInfo</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lock</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_entries</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">_entries</span><span class="p">.</span><span class="n" style="color: #333;">end</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>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">_entries</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="p">(</span><span class="n" style="color: #333;">u_int32_t</span><span class="p">)</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span><span class="n" style="color: #333;">nb</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">_synchro</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"><span class="p">}</span></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#9c52420fe937907fda5e3bd167986dd5f6434d76"><strong>gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +30,7 @@</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="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/misc/api/IProperty.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/system/api/ITime.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/system/impl/System.hpp></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="cp" style="color: #999; font-weight: 600;">#include <map></span></span>
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<pre style="margin: 0;"> <span id="LC36" 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">@@ -75,6 +76,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Default constructor. */</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">TimeInfo</span> <span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">TimeInfo</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Constructor taking a time factory.</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * \param[in] aTime : the time factory to be used.</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</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">@@ -126,6 +129,7 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC129" 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;">ITime</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_time</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC130" 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;">map</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="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_entriesT0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC131" 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;">map</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="n" style="color: #333;">u_int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_entries</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <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;">ISynchronizer</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="LC133" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#ebaa2f2e74863bc0d1c5240d9ff0ce14b78c270d"><strong>gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,9 +35,11 @@</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/collections/impl/IteratorFile.hpp></span></span>
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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 <gatb/tools/collections/impl/CollectionAbstract.hpp></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 <gatb/system/impl/System.hpp></span></span>
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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 <json/json.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" 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="LC45" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,18 +65,76 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Note (Rayan): this isn't very clean. Two files objectss are opened, one by BagFile (in write mode) and one in IterableFile (in read mode).</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * With Clang/OSX, turns out the IterableFile was created before BagFile, causing some troubles.</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Also this is opening the file twice, not nice. Anyway until I think of a better system, it's kept as it is, and IterableFile does a small hack*/</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="p">),</span> <span class="n" style="color: #333;">_name</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="LC68" class="line" lang="cpp"> <span class="p">),</span> <span class="n" style="color: #333;">_name</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_propertiesName</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">".props"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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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="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;">CollectionFile</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>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc tools::collections::Collection::remove */</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">remove</span> <span class="p">()</span> <span class="p">{</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;">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;">_name</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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">remove</span> <span class="p">()</span> <span class="p">{</span> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <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;">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;">_name</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <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;">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;">_propertiesName</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* R: some code duplication with GroupFile, but it's the same in the HDF5 case. not the best design.</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * so, collections can hold properties, so can groups.. */</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc tools::collections::Collection::addProperty */</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addProperty</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;">key</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;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "CollectionFile addProperty called, key=" << key << " value=" << value<< std::endl;</span></span>
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<pre style="margin: 0;">+<span id="LC88" 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;">ifstream</span> <span class="n" style="color: #333;">myfile</span> <span class="p">(</span><span class="n" style="color: #333;">_propertiesName</span><span class="p">);</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myfile</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">getline</span> <span class="p">(</span><span class="n" style="color: #333;">myfile</span><span class="p">,</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">myfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">JSON</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LoadJson</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise json is empty and we create it</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">.</span><span class="n" style="color: #333;">dump</span><span class="p">();</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">myfile2</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">myfile2</span><span class="p">.</span><span class="n" style="color: #333;">open</span> <span class="p">(</span><span class="n" style="color: #333;">_propertiesName</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">myfile2</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">myfile2</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="p">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc tools::collections::Collection::getProperty */</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" 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;">getProperty</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;">key</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "CollectionFile getProperty called, key=" << key << std::endl;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">myfile</span> <span class="p">(</span><span class="n" style="color: #333;">_propertiesName</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myfile</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="p">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">getline</span> <span class="p">(</span><span class="n" style="color: #333;">myfile</span><span class="p">,</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">myfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">JSON</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LoadJson</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">].</span><span class="n" style="color: #333;">ToString</span><span class="p">();</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="p">}</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="k" style="font-weight: 600;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_name</span><span class="p">;</span></span>
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137
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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;">string</span> <span class="n" style="color: #333;">_propertiesName</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"><span class="p">};</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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<li id="efdf123a4ecf95f1a9326ff6d3443694ceed944f">
<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#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="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">@@ -63,7 +63,7 @@ namespace impl {</td>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ok</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;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="mo" style="color: #099;">0755</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ok</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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65
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65
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<pre style="margin: 0;"> <span id="LC65" 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: can't create output directory ("</span> <span class="o" style="font-weight: 600;"><<</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" debug, doesexist:"</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;">doesExistDirectory</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">);</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"created directory "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">folder</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="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"created directory "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">folder</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="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// doesn't seem to be ever printed</span></span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="p">}</span> </span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="p">}</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We may need to create the HDF5 group. Empty name means root group, which is constructed by default. */</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="221" style="width: 35px; color: rgba(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">@@ -221,7 +221,7 @@ public:</td>
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>
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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 class="idiff left right">;</span></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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"."</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</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">// because gatb's getBaseName is stupid and cuts after the last dot</span></span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"></span>
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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;">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="LC227" 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>
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<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#318096db5deb1f35e51713c65641cded76fcd620"><strong>gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,6 +118,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">bloomCollection</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addProperty</span> <span class="p">(</span><span class="s" style="color: #d14;">"nb_hash"</span><span class="p">,</span> <span class="n" style="color: #333;">ss2</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">bloomCollection</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addProperty</span> <span class="p">(</span><span class="s" style="color: #d14;">"type"</span><span class="p">,</span> <span class="n" style="color: #333;">bloom</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getName</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">bloomCollection</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addProperty</span> <span class="p">(</span><span class="s" style="color: #d14;">"kmer_size"</span><span class="p">,</span> <span class="n" style="color: #333;">ss3</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">bloomCollection</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span> <span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// R: wasn't there before but I guess this can't hurt</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Load a Bloom filter from a group</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">@@ -62,14 +62,15 @@ class TestLeon : public Test</td>
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<pre style="margin: 0;"> <span id="LC62" 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;">TestLeon</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon3</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon4</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon5</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span><span class="p">(</span><span class="n" style="color: #333;">bank_checkLeon6</span><span class="p">);</span></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;"> CPPUNIT_TEST_GATB(bank_checkLeon7);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> CPPUNIT_TEST_GATB(bank_checkLeon8);*/</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="c1" style="color: #998; font-style: italic;">//removed some large files from distrib</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CPPUNIT_TEST_GATB(bank_checkLeon7);</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;">// CPPUNIT_TEST_GATB(bank_checkLeon8);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_SUITE_GATB_END</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" style="width: 35px; color: rgba(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">@@ -155,10 +156,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// STEP 2: compare reference and compressed version</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we open the files in read mode</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> </span>
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158
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<pre style="margin: 0;"> <span id="LC160" 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;">fasBank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Bank</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">open</span> <span class="p">(</span><span class="n" style="color: #333;">fastqFile</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//BankFasta</span></span>
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<pre style="margin: 0;"> <span id="LC161" 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;">leonBank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Bank</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">open</span> <span class="p">(</span><span class="n" style="color: #333;">leonFile</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//BankLeon</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">bank_compare_banks_equality</span><span class="p">(</span><span class="n" style="color: #333;">fasBank</span><span class="p">,</span> <span class="n" style="color: #333;">leonBank</span><span class="p">);</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> </span>
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162
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="p">}</span></span>
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163
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"></span>
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164
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<li id="fcfa76d64a82d58d9a219299e6272ce3d8768f9c">
<a href="https://salsa.debian.org/med-team/gatb-core/commit/8e45a9a10a24b387c839913a974e40f9dff2c517#fcfa76d64a82d58d9a219299e6272ce3d8768f9c"><strong>gatb-core/test/unit/src/bcalm/TestBcalm.cpp</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*****************************************************************************</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * GATB : Genome Assembly Tool Box</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This program is free software: you can redistribute it and/or modify</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU Affero General Public License as</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * published by the Free Software Foundation, either version 3 of the</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC9" 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="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * GNU Affero General Public License for more details.</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU Affero General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*****************************************************************************/</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <CppunitCommon.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/system/impl/System.hpp></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/math/LargeInt.hpp></span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/collections/impl/IteratorFile.hpp></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/misc/api/StringsRepository.hpp></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/misc/impl/TimeInfo.hpp></span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/bcalm2/unionFind.hpp></span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/designpattern/impl/Command.hpp></span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/designpattern/impl/IteratorHelpers.hpp></span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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36
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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 <thread></span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" 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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" 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;">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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">misc</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="p">;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC43" 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;">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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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;">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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</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="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" 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;">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;">impl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">math</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</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;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</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;">DBPATH</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;">a</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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 class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">tests</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC57" 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="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** \brief Test class for genomic databases management</span></span>
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<pre style="margin: 0;">+<span id="LC60" 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="LC61" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestBcalm</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Test</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC63" 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="LC64" 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;">TestBcalm</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">bcalm_test1</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_TEST_SUITE_GATB_END</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></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;">/********************************************************************************/</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setUp</span> <span class="p">()</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">tearDown</span> <span class="p">()</span> <span class="p">{}</span></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;">/********************************************************************************/</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;">void</span> <span class="n" style="color: #333;">bcalm_test1</span> <span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;">// i wanna test de UF because it was buggy in multithreads</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_uf_elts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3000000</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">unionFind</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uf</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_elts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">doJoins</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;">uf</span><span class="p">](</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</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;">end</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="p">{</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">uf</span><span class="p">.</span><span class="n" style="color: #333;">union_</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "joining " << i << " " << i+1 << std::endl; // it's indeed threaded, this checks it</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="p">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="p">};</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//doJoins(0,nb_uf_elts/2);</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//doJoins(nb_uf_elts/2,nb_uf_elts-1);</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span> <span class="n" style="color: #333;">first</span><span class="p">(</span><span class="n" style="color: #333;">doJoins</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">nb_uf_elts</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span> <span class="n" style="color: #333;">second</span><span class="p">(</span><span class="n" style="color: #333;">doJoins</span><span class="p">,</span><span class="n" style="color: #333;">nb_uf_elts</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_elts</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">));</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span> <span class="n" style="color: #333;">third</span><span class="p">(</span><span class="n" style="color: #333;">doJoins</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_elts</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">),</span><span class="n" style="color: #333;">nb_uf_elts</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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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">third</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">foundclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">// not always 0, depends which thread starts first</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</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_elts</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="p">{</span> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ufclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ufclass</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">foundclass</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="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;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">class of "</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="s" style="color: #d14;">" is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ufclass</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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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">CPPUNIT_ASSERT</span> <span class="p">(</span><span class="n" style="color: #333;">ufclass</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">foundclass</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"><span class="p">};</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="n" style="color: #333;">CPPUNIT_TEST_SUITE_REGISTRATION</span> <span class="p">(</span><span class="n" style="color: #333;">TestBcalm</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="n" style="color: #333;">CPPUNIT_TEST_SUITE_REGISTRATION_GATB</span> <span class="p">(</span><span class="n" style="color: #333;">TestBcalm</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="p">}</span> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end of namespaces. */</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"></span></pre>
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