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GitLab

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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/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17">8febe06b</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-08-17T20:09:04Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.1+git20190813.a73b6dd+dfsg</pre>

</li>

</ul>

<h4>28 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#31c00ce3cbe73348c779c23d6f94b9a7b382424d">

gatb-core/.gitignore

</a>

</li>

<li class="file-stats">

<a href="#4c007bda60857aed5186f73b4dd88ee753952d0d">

gatb-core/CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#fcdbdfd0b8e9a912c8709fe8501b9aed1259558e">

gatb-core/examples/Makefile

</a>

</li>

<li class="file-stats">

<a href="#6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33">

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

</a>

</li>

<li class="file-stats">

<a href="#490f86cdfc07e7db3455fffd8859052bd5dbeb50">

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

</a>

</li>

<li class="file-stats">

<a href="#13ea1c05cb7d9ae8ed463fc61e80763d1ced17a4">

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

</a>

</li>

<li class="file-stats">

<a href="#a434192ac5c383bb512502817a95c4f4cc9378dc">

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

</a>

</li>

<li class="file-stats">

<a href="#2ff315124cb4ed9eebb9d35c35743144de29a781">

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

</a>

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<li class="file-stats">

<a href="#a57dcb64f25d9850b62e0fd29229dc775bc27187">

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

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<li class="file-stats">

<a href="#c8b46ef3dbdf675bf383053ecb5973e97e8abe00">

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

</a>

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<li class="file-stats">

<a href="#34ae9ab374303a1000194fa7d58aeba9d58f32ce">

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

</a>

</li>

<li class="file-stats">

<a href="#8d46876b0b01c8687ffec95a3e56a84f1d5ffc83">

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

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<li class="file-stats">

<a href="#3d59b6581d3871516a6b55261db0dac87fd2a525">

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

</a>

</li>

<li class="file-stats">

<a href="#b5330caa1a1248a1b6246d8caa9f656b0e8218c1">

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

</a>

</li>

<li class="file-stats">

<a href="#4dce1e5207210c91bde58be44fc7ca206c6fa1e7">

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

</a>

</li>

<li class="file-stats">

<a href="#1585bdf1cfb187c932725cb3cea90f0f3a5efa7e">

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

</a>

</li>

<li class="file-stats">

<a href="#7026e2876c610bcf71aa5114af58599b6d8a4f13">

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

</a>

</li>

<li class="file-stats">

<a href="#a8c2c0b48f4fe5a6db4d07e69030b1be23067359">

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

</a>

</li>

<li class="file-stats">

<a href="#594afd8796d14815b648e15a5aa082a670521b57">

gatb-core/src/gatb/kmer/impl/Model.hpp

</a>

</li>

<li class="file-stats">

<a href="#c96a868ed336609b4f21c39702ce23f33c3e7850">

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

</a>

</li>

<li class="file-stats">

<a href="#8c129eb4ed08a953123df6cf51c678096ab15153">

gatb-core/src/gatb/kmer/impl/PartiInfo.hpp

</a>

</li>

<li class="file-stats">

<a href="#d6e7c785a22fb981430b2e12eed55480273715bf">

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

</a>

</li>

<li class="file-stats">

<a href="#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4">

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

</a>

</li>

<li class="file-stats">

<a href="#4c12716c6fcb516eda353ab99ab2b81002b77515">

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

</a>

</li>

<li class="file-stats">

<a href="#6805524260d80eecf62b8e8407368389214b1fde">

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

</a>

</li>

<li class="file-stats">

<a href="#9a3c9915f167211d4a7ca96fe03df76f04a8c369">

gatb-core/src/gatb/tools/misc/impl/Histogram.hpp

</a>

</li>

<li class="file-stats">

<a href="#4258957fbedcdb09fe6853db03d786c2be1fbc78">

gatb-core/src/gatb/tools/misc/impl/Pool.hpp

</a>

</li>

<li class="file-stats">

<a href="#440041d1ca70d3a1c65ca98b83f363a9cafd5a9e">

gatb-core/test/jenkins/test-suite-fedora20-gcc-4.8.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="31c00ce3cbe73348c779c23d6f94b9a7b382424d">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#31c00ce3cbe73348c779c23d6f94b9a7b382424d"><strong>gatb-core/.gitignore</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,4 +4,8 @@ CMakeLists.txt.user</td>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">/.cproject</span>

</pre>

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

5

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">*.leon</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.DS_Store</span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">thirdparty/hdf5/src/H5Edefin.h</span>

</pre>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">thirdparty/hdf5/src/H5Einit.h</span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">thirdparty/hdf5/src/H5Epubgen.h</span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">thirdparty/hdf5/src/H5Eterm.h</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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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">

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="4c007bda60857aed5186f73b4dd88ee753952d0d">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#4c007bda60857aed5186f73b4dd88ee753952d0d"><strong>gatb-core/CMakeLists.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

1

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

1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>gatb-core<span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># We set the required version</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="4" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span> <span class="p">(</span>VERSION 3.1.0<span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span> <span class="p">(</span>VERSION 3.1<span class="idiff left right">0</span>.0<span class="p">)</span></span>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(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="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The version number.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(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="211" style="width: 35px; color: rgba(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">@@ -211,7 +211,7 @@ set (gatb-core-flags ${LIBRARY_COMPILE_DEFINITIONS})</td>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>gatb-core-includes <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/include  <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/include/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_BUILD_TYPE</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/src  <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/thirdparty <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">gatb-core-extra-libraries-inc</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># We define the libraries used for linking binary based on gatb core</span></span>

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<td class="diff-line-num new_line old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5 <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">gatb-core-extra-libraries</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="215" 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="LC214" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5<span class="idiff left right">-static</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">gatb-core-extra-libraries</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(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="LC216" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># We define the directory where to find cmake helpers</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(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="LC217" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>gatb-core-cmake  <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_MODULE_PATH</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -257,7 +257,7 @@ ADD_SUBDIRECTORY(thirdparty)</td>

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<td class="diff-line-num old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#  DEPENDENCIES </span></span>

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<td class="diff-line-num old_line" data-linenumber="258" style="width: 35px; color: rgba(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="LC258" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># we must be sure that hdf5 is built and installed before building gatb-core</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="260" 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="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ADD_DEPENDENCIES</span> <span class="p">(</span>gatbcore-static hdf5 hdf5_postbuild<span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="261" 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="260" 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="LC260" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ADD_DEPENDENCIES</span> <span class="p">(</span>gatbcore-static hdf5<span class="idiff left right">-static</span> hdf5_postbuild<span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cmake"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>

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<td class="diff-line-num old_line" data-linenumber="263" style="width: 35px; color: rgba(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="263" style="width: 35px; color: rgba(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="LC263" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#  DOCUMENTATION GENERATION </span></span>

</pre>

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<li id="fcdbdfd0b8e9a912c8709fe8501b9aed1259558e">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#fcdbdfd0b8e9a912c8709fe8501b9aed1259558e"><strong>gatb-core/examples/Makefile</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ GATB=$(shell pwd)/../</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">GATB_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(GATB)</span>/build/lib</span>

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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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span>  <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nt" style="color: #000080;">-O3</span>  <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(GATB)</span>/src  <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(GATB)</span>/build/include <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(GATB)</span>/thirdparty </span>

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<td class="diff-line-num old old_line" data-linenumber="11" 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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">=</span>   <span class="nt" style="color: #000080;">-L</span><span class="nv" style="color: #008080;">$(GATB_LIB)</span> <span class="nt" style="color: #000080;">-lgatbcore</span>  <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-l<span class="idiff left">z</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-lhdf5</span></span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nt" style="color: #000080;">-ldl</span> <span class="nt" style="color: #000080;">-static</span></span>

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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">=</span>   <span class="nt" style="color: #000080;">-L</span><span class="nv" style="color: #008080;">$(GATB_LIB)</span> <span class="nt" style="color: #000080;">-lgatbcore</span>  <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-l<span class="idiff left">hdf5</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-lz</span></span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nt" style="color: #000080;">-ldl</span> <span class="nt" style="color: #000080;">-static</span></span>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>

</pre>

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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">

13

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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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>

</pre>

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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="make"><span class="nv" style="color: #008080;">SRCS</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard <span class="k" style="font-weight: 600;">*</span>.cpp<span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<li id="6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#6861fd4c43e7c21bb057ecc2ad7a189b8aaf5b33"><strong>gatb-core/src/gatb/bank/impl/BankFasta.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(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">@@ -58,7 +58,7 @@ typedef struct</td>

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="cpp">    <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">stream</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buffer</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="61" 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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">buffer_start</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_end</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="62" 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="61" 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="LC61" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64_</span>t</span> <span class="n" style="color: #333;">buffer_start</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_end</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">eof</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">last_char</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(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">@@ -79,7 +79,7 @@ struct variable_string_t</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">     <span class="n" style="color: #333;">variable_string_t</span> <span class="p">()</span>  <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">variable_string_t</span> <span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">);</span> <span class="p">}</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">max</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64_</span>t</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">max</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">    <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;">string</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>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(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="433" style="width: 35px; color: rgba(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">@@ -433,7 +433,7 @@ inline signed int buffered_gets (</td>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_start</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</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="LC434" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64_</span>t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_start</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">rebuffer</span> <span class="p">(</span><span class="n" style="color: #333;">bf</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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438

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allow_spaces</span><span class="p">)</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="452" style="width: 35px; color: rgba(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="452" style="width: 35px; color: rgba(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">@@ -452,6 +452,7 @@ inline signed int buffered_gets (</td>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_power_of_2</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span><span class="p">))</span>  <span class="p">{</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="p">}</span></span>

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453

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp">            <span class="n" style="color: #333;">nearest_power_of_2</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span><span class="p">);</span></span>

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454

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp">            <span class="n" style="color: #333;">s</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span>  <span class="n" style="color: #333;">REALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">s</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;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "realloc of size " << s->max << " res: " << (uint64_t)(s->string) << std::endl;</span></span>

</pre>

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455

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp">        <span class="p">}</span></span>

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456

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp">         <span class="n" style="color: #333;">memcpy</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_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;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_start</span><span class="p">);</span></span>

</pre>

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457

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp">        <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer_start</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="765" style="width: 35px; color: rgba(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="766" style="width: 35px; color: rgba(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">@@ -765,7 +766,7 @@ void BankFasta::Iterator::estimate (u_int64_t& number, u_int64_t& totalSize, u_i</td>

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766

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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// linear extrapolation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="767" style="width: 35px; color: rgba(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="LC768" class="line" lang="cpp">        <span class="n" style="color: #333;">number</span>    <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">number</span>    <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_ref</span><span class="p">.</span><span class="n" style="color: #333;">getSize</span><span class="p">())</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">actualPosition</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="768" 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="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp">        <span class="n" style="color: #333;">totalSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">totalSize</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">_ref</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getSize</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 right">actualPosition</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp">        <span class="n" style="color: #333;">totalSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">totalSize</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">_ref</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getSize</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="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">actualPosition</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="772" style="width: 35px; color: rgba(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="LC772" class="line" lang="cpp"></span>

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<br>

</li>

<li id="490f86cdfc07e7db3455fffd8859052bd5dbeb50">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#490f86cdfc07e7db3455fffd8859052bd5dbeb50"><strong>gatb-core/src/gatb/bcalm2/bglue_algo.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,10 +60,18 @@ using namespace gatb::core::tools::dp::impl;</td>

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<pre style="margin: 0;"> <span id="LC60" 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="p">;</span></span>

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61

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61

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<pre style="margin: 0;"> <span id="LC61" 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>

</pre>

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62

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"></span>

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64

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"></span>

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65

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

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// let's be clear here:</span></span>

</pre>

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

</pre>

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// but there can be more than 2^{32} sequences in the glue file</span></span>

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<td class="diff-line-num new new_line" data-linenumber="69" 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="LC69" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">seq_idx_t</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="70" 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="LC70" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// so, potentially, more than 2^{32} UF hashes (but not necessarily, consider that some sequences don't need to be glued)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// let's hope that there won't be saturation (only 1 UF class with all unitigs)</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if this happens, then "Top 10 glue partitions by size:" will show only one entry and BCALM will blow up in memory</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// a fix would be to use a 64 bits UF (to be coded later)</span></span>

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

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="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;">core</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">debruijn</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">impl</span>  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(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">@@ -189,18 +197,17 @@ static string skip_first_abundance(const string& list)</td>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">markedSeq</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// there used to be "string seq; string abundance" but i noticed that i did not need that info for determining the chain of glues. not much space saved though (like 10-20%). I suppose the biggest memory-hog is the ks/ke unordered_map</span></span>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lmark</span><span class="p">,</span> <span class="n" style="color: #333;">rmark</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">Type</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp">    <span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">ks</span><span class="p">,</span> <span class="n" style="color: #333;">ke</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// [start,end] kmers of seq, in canonical form (redundant information with seq, but helpful)</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp">    <span class="n" style="color: #333;">markedSeq</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lmark</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rmark</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ks</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ke</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">rc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">lmark</span><span class="p">(</span><span class="n" style="color: #333;">lmark</span><span class="p">),</span> <span class="n" style="color: #333;">rmark</span><span class="p">(</span><span class="n" style="color: #333;">rmark</span><span class="p">),</span> <span class="n" style="color: #333;">ks</span><span class="p">(</span><span class="n" style="color: #333;">ks</span><span class="p">),</span> <span class="n" style="color: #333;">ke</span><span class="p">(</span><span class="n" style="color: #333;">ke</span><span class="p">)</span> <span class="p">{};</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">    <span class="n" style="color: #333;">markedSeq</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lmark</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rmark</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ks</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Type</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ke</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">rc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">lmark</span><span class="p">(</span><span class="n" style="color: #333;">lmark</span><span class="p">),</span> <span class="n" style="color: #333;">rmark</span><span class="p">(</span><span class="n" style="color: #333;">rmark</span><span class="p">),</span> <span class="n" style="color: #333;">ks</span><span class="p">(</span><span class="n" style="color: #333;">ks</span><span class="p">),</span> <span class="n" style="color: #333;">ke</span><span class="p">(</span><span class="n" style="color: #333;">ke</span><span class="p">)</span> <span class="p">{};</span></span>

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

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">revcomp</span><span class="p">()</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -213,22 +220,22 @@ struct markedSeq</td>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// hack to refer to a sequences in msInPart as reverse complemented</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint32</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;"><span class="idiff left">seq_idx_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_idx</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">index</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="219" 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="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">((<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff">63</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="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff right">)</span></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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<td class="diff-line-num new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

220

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<td class="diff-line-num new_line" data-linenumber="227" style="width: 35px; color: rgba(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="LC227" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_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">

221

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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" 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="229" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint32</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;"><span class="idiff left">seq_idx_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_idx</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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

<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="224" style="width: 35px; color: rgba(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="231" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_rev_index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="225" style="width: 35px; color: rgba(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="232" style="width: 35px; color: rgba(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="LC232" class="line" lang="cpp">    <span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: glue sequence index too large "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">index</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="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="226" 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="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="mi" style="color: #099;"><span class="idiff right">31</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff right">63</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="227" style="width: 35px; color: rgba(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="234" style="width: 35px; color: rgba(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="LC234" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="228" style="width: 35px; color: rgba(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="235" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="229" 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="236" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint32</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="236" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;"><span class="idiff left">seq_idx_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_rev_index</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">seq_idx</span>_t</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="230" style="width: 35px; color: rgba(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="237" style="width: 35px; color: rgba(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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">((</span><span class="mi" style="color: #099;"><span class="idiff left">1LL</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="mi" style="color: #099;"><span class="idiff">31</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="mi" style="color: #099;"><span class="idiff right">1LL</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">((<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff">63</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="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//typedef lazy::memory::buffer_allocator<markedSeq> custom_allocator_t;</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">@@ -238,25 +245,27 @@ static uint32_t no_rev_index(uint32_t index)</td>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * output: res, a list of lists of sequences that will be glued together</span></span>

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<pre style="margin: 0;"> <span id="LC246" 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="LC247" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">determine_order_sequences</span><span class="p">(</span><span class="n" style="color: #333;">vector</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="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">res</span></span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">markedSeq</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">markedSequences</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">determine_order_sequences</span><span class="p">(</span><span class="n" style="color: #333;">vector</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;"><span class="idiff left">seq_idx_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">res_is_circular</span></span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">markedSeq</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">markedSequences</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span> <span class="n" style="color: #333;">Type</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">    <span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kmerIndex</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">usedSeq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left">nsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">in</span>t</span> <span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="247" 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="LC251" class="line" lang="cpp">    <span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kmerIndex</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="247" 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="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">usedSeq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="247" 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="253" 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="LC253" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int64_</span>t</span> <span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// index kmers to their seq</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// kmerIndex associates a kmer extremity to its index in markedSequences</span></span>

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<pre style="margin: 0;">-<span id="LC250" 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;"><span class="idiff left right">uint32</span>_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;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_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;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp">        <span class="n" style="color: #333;">kmerIndex</span><span class="p">[</span><span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ks</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp">        <span class="n" style="color: #333;">kmerIndex</span><span class="p">[</span><span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ke</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">glue_from_extremity</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">](</span><span class="n" style="color: #333;">markedSeq</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;">current</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chain_index</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint32</span>_t</span> <span class="n" style="color: #333;">markedSequence_index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expect_circular</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">glue_from_extremity</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">](</span><span class="n" style="color: #333;">markedSeq</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;">current</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">seq_idx_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chain_index</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">seq_idx</span>_t</span> <span class="n" style="color: #333;">markedSequence_index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expect_circular</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">first_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequence_index</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp">        <span class="n" style="color: #333;">vector</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;">chain</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp">        <span class="n" style="color: #333;">seq_idx_t</span> <span class="n" style="color: #333;">first_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequence_index</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seq_idx_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chain</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp">        <span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">chain_index</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rmark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">rmark</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">@@ -268,14 +277,14 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC277" 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;">"current ke "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">ke</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" index "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">no_rev_index</span><span class="p">(</span><span class="n" style="color: #333;">chain_index</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" markings: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">lmark</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">rmark</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="LC278" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// this sequence has a rmark, so necessarily there is another sequence to glue it with. find it here.</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp">            <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">candidateSuccessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerIndex</span><span class="p">[</span><span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">ke</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">            <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">candidateSuccessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerIndex</span><span class="p">[</span><span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">ke</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp">           </span>

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<td class="diff-line-num old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">            <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">candidateSuccessors</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">markedSequence_index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">candidateSuccessors</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// remove the current seq from our indexing data structure </span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp">            <span class="n" style="color: #333;">candidateSuccessors</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">markedSequence_index</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp">            <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">candidateSuccessors</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;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// normally there is exactly one sequence to glue with</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">successor_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">candidateSuccessors</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// pop()</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">            <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">successor_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">candidateSuccessors</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// pop()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp">            <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">successor_index</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">markedSequence_index</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp">            <span class="n" style="color: #333;">markedSeq</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;">successor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">successor_index</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(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="324" style="width: 35px; color: rgba(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">@@ -315,6 +324,11 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">usedSeq</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">markedSequence_index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">usedSeq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">                <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp">                    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">markedSequence_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">first_index</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="318" 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="LC327" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" 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;">"breaking at circular unitig"</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="LC329" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">// here it would be tempting to remove the last element of the chain to remove the last kmer</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">// but this strategy doesn't work as that element might be longer than a kmer </span></span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">// so the preferred strategy is to cut the last nucleotide of a circular unitig</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp">            <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">@@ -329,11 +343,12 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp">        <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp">        <span class="n" style="color: #333;">res_is_circular</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">expect_circular</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">        <span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chain</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="LC348" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// iterate<span class="idiff left right">d</span> markedSequences, and picks extremities of a chain</span></span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// iterate markedSequences, and picks extremities of a chain</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</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;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC353" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp">        <span class="n" style="color: #333;">markedSeq</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;">current</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="352" style="width: 35px; color: rgba(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="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,7 +367,7 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/* normalize sequence so that lmark is false */</span></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">chain_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">chain_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">index</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">lmark</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp">            <span class="n" style="color: #333;">current</span><span class="p">.</span><span class="n" style="color: #333;">revcomp</span><span class="p">();</span> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -365,13 +380,13 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="382" style="width: 35px; color: rgba(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="LC382" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">special case: a circular unitig, to be glued with multiple sequences all containing doubled kmers at extremities</span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="369" 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="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">my fix plan: we pick an extremity at random, and chop the last nucleotide and mark it to not be glued. also find the corresponding kmer in other extremity, and mark it as not to be glued</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="370" 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="383" 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="LC383" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">handle the special cases undetected in the previous loop: </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="370" 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="384" 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="LC384" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">they are circular unitigs, to be glued with other sequences all containing doubled kmers at extremities</span></span></span>

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<td class="diff-line-num new_line" data-linenumber="385" style="width: 35px; color: rgba(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="LC385" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "nb chained " << nb_chained << " markedseq size" << markedSequences.size() << std::endl;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">remaining_indices</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC374" 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;"><span class="idiff left right">uint32</span>_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;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="375" 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="388" 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="LC388" class="line" lang="cpp">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx_</span>t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">remaining_indices</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="375" 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="389" 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="LC389" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_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;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">usedSeq</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 class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">usedSeq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">                <span class="n" style="color: #333;">remaining_indices</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -380,23 +395,17 @@ static void determine_order_sequences(vector<vector<uint32_t>> &res, const vecto</td>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">remaining_indices</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="382" style="width: 35px; color: rgba(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="397" style="width: 35px; color: rgba(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="LC397" class="line" lang="cpp">        <span class="n" style="color: #333;">markedSeq</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;">current</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">remaining_indices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]];</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">chain_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">remaining_indices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="384" 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="398" 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="LC398" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">chain_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">[</span><span class="n" style="color: #333;">remaining_indices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp">        <span class="n" style="color: #333;">glue_from_extremity</span><span class="p">(</span><span class="n" style="color: #333;">current</span><span class="p">,</span> <span class="n" style="color: #333;">chain_index</span><span class="p">,</span> <span class="n" style="color: #333;">remaining_indices</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">markedSequences</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="LC389" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC390" 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;">" Note: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">markedSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nb_chained</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" sequence chunks not returned in output unitigs (likely small circular contigs)"</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="LC391" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// assert(sequences.size() == nb_chained); // make sure we've scheduled to glue all sequences in this partition</span></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* straightforward glueing of a chain</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="405" style="width: 35px; color: rgba(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="LC405" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * sequences should be ordered and in the right orientation</span></span>

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * so, it'<span class="idiff left right"> just a matter of chopping of the first kmer</span></span></span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * so, it'<span class="idiff left right">s just a matter of chopping of the first kmer of elements i>1 of each chain</span></span></span>

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<pre style="margin: 0;"> <span id="LC407" 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="LC399" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">glue_sequences</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">chain</span></span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">abundances</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res_seq</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res_abundances</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">glue_sequences</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">seq_idx_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">chain</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">is_circular</span></span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">abundances</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res_seq</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">res_abundances</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(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="415" style="width: 35px; color: rgba(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">@@ -406,7 +415,7 @@ static void glue_sequences(vector<uint32_t> &chain, std::vector<std::string> &se</td>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"glueing new chain: "</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chain</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;">chain</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp">    <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32</span>_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</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="LC418" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</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="LC419" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="420" style="width: 35px; color: rgba(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="LC420" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">no_rev_index</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">)];</span></span>

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<td class="diff-line-num old_line" data-linenumber="412" style="width: 35px; color: rgba(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="LC421" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">abs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abundances</span><span class="p">[</span><span class="n" style="color: #333;">no_rev_index</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">)];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="443" style="width: 35px; color: rgba(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">@@ -434,7 +443,24 @@ static void glue_sequences(vector<uint32_t> &chain, std::vector<std::string> &se</td>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp">        <span class="n" style="color: #333;">previous_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">substr</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="n" style="color: #333;">k</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="435" style="width: 35px; color: rgba(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="444" style="width: 35px; color: rgba(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="LC444" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">previous_kmer</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

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445

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="437" 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">

437

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<td class="diff-line-num new_line old" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" 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="446" 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">

446

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_circular</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="447" 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">

447

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="448" 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">

448

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="449" 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">

449

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res_seq</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="450" 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">

450

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

<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res_abundances</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="451" 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">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// trick: do it with the first kmer instead</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="452" 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">

452

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp">        <span class="n" style="color: #333;">res_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc</span><span class="p">(</span><span class="n" style="color: #333;">res_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="453" 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">

453

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp">        <span class="n" style="color: #333;">res_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_abundances</span><span class="p">(</span><span class="n" style="color: #333;">res_abundances</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="454" 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">

454

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" 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="455" 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">

455

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp">        <span class="n" style="color: #333;">res_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res_seq</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="456" 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">

456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp">        <span class="n" style="color: #333;">res_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skip_first_abundance</span><span class="p">(</span><span class="n" style="color: #333;">res_abundances</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" 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="457" 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">

457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" 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="458" 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">

458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp">        <span class="n" style="color: #333;">res_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc</span><span class="p">(</span><span class="n" style="color: #333;">res_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="459" 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">

459

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp">        <span class="n" style="color: #333;">res_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_abundances</span><span class="p">(</span><span class="n" style="color: #333;">res_abundances</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" 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="460" 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">

460

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res_seq</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res_abundances</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="LC462" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="463" 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="LC463" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="464" style="width: 35px; color: rgba(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="LC464" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(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="505" style="width: 35px; color: rgba(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">@@ -479,8 +505,6 @@ class hasher_t</td>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">partition_t</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* computes and uniquifies the hashes of marked kmers at extremities of all to-be-glued sequences */</span></span>

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<td class="diff-line-num new_line" data-linenumber="509" style="width: 35px; color: rgba(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="LC509" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prepare_uf</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">IBank</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">&</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;">pass</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_elts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">estimated_nb_glue_sequences</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="489" style="width: 35px; color: rgba(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="513" style="width: 35px; color: rgba(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">@@ -489,7 +513,7 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<pre style="margin: 0;"> <span id="LC513" 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;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">;</span> </span>

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp">    <span class="n" style="color: #333;">nb_marked_extremities</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;">nb_unmarked_extremities</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

491

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<td class="diff-line-num new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

515

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="492" 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">

492

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<td class="diff-line-num new_line old" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">partition_t</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="493" 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="516" 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">

516

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes_t</span></span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<td class="diff-line-num new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

517

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<td class="diff-line-num new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

518

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// relatively accurate number of sequences to be inserted</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="diff-line-num new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

519

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<pre style="margin: 0;"> <span id="LC519" 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;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" style="width: 35px; color: rgba(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="521" style="width: 35px; color: rgba(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">@@ -497,7 +521,7 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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<td class="diff-line-num new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

521

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(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="522" style="width: 35px; color: rgba(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="LC522" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/* class (formerly a simple lambda function) to process a kmer and decide which bucket(s) it should go to */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<td class="diff-line-num new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

523

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/* needed to make it a class because i want it to remember its thread index */</span></span>

</pre>

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500

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<td class="diff-line-num new_line old" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">UniquifyKey</span>s</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="524" 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">

524

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">RepartHashe</span>s</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

525

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

502

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<td class="diff-line-num new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

526

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelCanonical</span> <span class="n" style="color: #333;">ModelCanon</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<td class="diff-line-num new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

527

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="506" style="width: 35px; color: rgba(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="530" style="width: 35px; color: rgba(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">@@ -506,13 +530,13 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<td class="diff-line-num new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

530

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp">        <span class="n" style="color: #333;">ModelCanon</span> <span class="n" style="color: #333;">modelCanon</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

507

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<td class="diff-line-num new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp">        <span class="n" style="color: #333;">Hasher_T</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ModelCanon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hasher</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(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="LC532" 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;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="509" 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">

509

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<td class="diff-line-num new_line old" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">partition_t</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" 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">

533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes_t</span></span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<td class="diff-line-num new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

534

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_currentThreadIndex</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

511

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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

512

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<td class="diff-line-num new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp">        <span class="nl">public:</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="513" 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">

513

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<td class="diff-line-num new_line old" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left right">UniquifyKey</span>s</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="514" 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="537" 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">

537

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp">        <span class="n" style="color: #333;"><span class="idiff left right">RepartHashe</span>s</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

514

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<td class="diff-line-num new_line" data-linenumber="538" style="width: 35px; color: rgba(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="LC538" 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;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_marked_extremities</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;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="515" 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">

515

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<td class="diff-line-num new_line old" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">partition_t</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uf_hashes_vectors</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="539" 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">

539

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

<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes_t</span></span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uf_hashes_vectors</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

516

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<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp">                     <span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">k</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">),</span> <span class="n" style="color: #333;">pass</span><span class="p">(</span><span class="n" style="color: #333;">pass</span><span class="p">),</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">(</span><span class="n" style="color: #333;">nb_passes</span><span class="p">),</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">),</span> <span class="n" style="color: #333;">modelCanon</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">),</span> <span class="n" style="color: #333;">hasher</span><span class="p">(</span><span class="n" style="color: #333;">modelCanon</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

517

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<td class="diff-line-num new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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

<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp">                        <span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">(</span><span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">),</span> <span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">(</span><span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

518

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<td class="diff-line-num new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

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

<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp">                         <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">(</span><span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">),</span> <span class="n" style="color: #333;">_currentThreadIndex</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -529,12 +553,13 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lmark</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp">            <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="531" style="width: 35px; color: rgba(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="LC555" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmerBegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">UF of </span>canonical kmers in ModelCanon form, then hashed</span></span>

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// canonical kmers in ModelCanon form, then hashed</span></span>

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<pre style="margin: 0;"> <span id="LC557" 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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<td class="diff-line-num new_line" data-linenumber="558" style="width: 35px; color: rgba(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="LC558" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</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="LC559" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span><span class="n" style="color: #333;">nb_passes</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span><span class="n" style="color: #333;">pass</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp">                <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cpp">                    <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">[</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">h1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp">                    <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">[</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">h1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// this is where the 64 bits "hasher() result" to the 32 bits "uf_hash_t" conversion is taking place</span></span>

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp">                                                             <span class="c1" style="color: #998; font-style: italic;">// but hopefully it's okay </span></span>

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp">                    <span class="n" style="color: #333;">nb_marked_extremities</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="579" style="width: 35px; color: rgba(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="604" style="width: 35px; color: rgba(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">@@ -579,10 +604,10 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"></span>

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580

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<td class="diff-line-num new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<pre style="margin: 0;"> <span id="LC605" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="582" 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">

582

</td>

<td class="diff-line-num new_line old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left">UniquifyKeys</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">uniquifyKey</span>s</span><span class="p">(</span><span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" 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">

607

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left">RepartHashes</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">repartHashe</span>s</span><span class="p">(</span><span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp">                              <span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

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<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp">                              <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="585" 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">

585

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<td class="diff-line-num new_line old" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC585" 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;"><span class="idiff left right">uniquifyKey</span>s</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="610" 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">

610

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<pre style="margin: 0;">+<span id="LC610" 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;"><span class="idiff left right">repartHashe</span>s</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(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="LC611" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</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;">nb_marked_extremities</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" marked kmers, "</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_unmarked_extremities</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" unmarked kmers"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<pre style="margin: 0;"> <span id="LC612" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="593" style="width: 35px; color: rgba(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="618" style="width: 35px; color: rgba(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">@@ -593,7 +618,7 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

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<td class="diff-line-num new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

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<pre style="margin: 0;"> <span id="LC618" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">        prepareUF(it->item());*/</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="594" style="width: 35px; color: rgba(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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="595" style="width: 35px; color: rgba(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="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="596" 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="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"created vector of hashes, size approx "</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;">to_string</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">partition</span>_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="621" 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="LC621" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"created vector of hashes, size approx "</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;">to_string</span><span class="p">(</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes</span>_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nb_marked_extremities</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">()</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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<td class="diff-line-num new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<pre style="margin: 0;"> <span id="LC622" class="line" lang="cpp">    <span class="n" style="color: #333;">ThreadPool</span> <span class="n" style="color: #333;">uf_sort_pool</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// ThreadPool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<td class="diff-line-num new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//  ctpl::thread_pool uf_merge_pool(nb_threads);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

</td>

<td class="diff-line-num new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="602" style="width: 35px; color: rgba(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="627" style="width: 35px; color: rgba(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">@@ -602,7 +627,7 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="diff-line-num new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<td class="diff-line-num new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sortuniq</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_hashes_vectors</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_id</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="605" 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">

605

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<td class="diff-line-num new_line old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">partition</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" 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">

630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp">            <span class="n" style="color: #333;">sort</span><span class="p">(</span> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

607

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<td class="diff-line-num new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp">            <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span> <span class="n" style="color: #333;">unique</span><span class="p">(</span> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="p">),</span> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="613" style="width: 35px; color: rgba(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="638" style="width: 35px; color: rgba(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">@@ -613,13 +638,16 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<td class="diff-line-num old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

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<td class="diff-line-num new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

614

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<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp">    <span class="n" style="color: #333;">uf_sort_pool</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// ThreadPool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

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<td class="diff-line-num new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="616" 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">

616

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<td class="diff-line-num new_line old" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp">    </span>

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<td class="diff-line-num old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

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<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(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="LC641" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// a single-threaded merge and write to file before they're loaded again in bglue</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="618" 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">

618

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<td class="diff-line-num new_line old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp">    <span class="n" style="color: #333;">BagFile</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bagf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BagFile</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="p">(</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.hashes."</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;">pass</span><span class="p">));</span> <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">bagf</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="619" 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">

619

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<td class="diff-line-num new_line old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp">  <span class="n" style="color: #333;">Bag</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">currentbag</span> <span class="o" style="font-weight: 600;">=</span>  <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BagCache</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="p">(</span>  <span class="n" style="color: #333;">bagf</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span> <span class="p">);</span> <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">currentbag</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">// really? we have to through these hoops to do a simple binary file in gatb? gotta change this.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="620" 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">

620

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<td class="diff-line-num new_line old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_elts_pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" 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="642" 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">

642

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp">    <span class="n" style="color: #333;">BagFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bagf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BagFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.hashes."</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;">pass</span><span class="p">));</span> <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">bagf</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="643" 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">

643

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp">  <span class="n" style="color: #333;">Bag</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">currentbag</span> <span class="o" style="font-weight: 600;">=</span>  <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BagCache</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span>  <span class="n" style="color: #333;">bagf</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span> <span class="p">);</span> <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">currentbag</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">// really? we have to through these hoops to do a simple binary file in gatb? gotta change this.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" 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="644" 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">

644

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" 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="645" 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">

645

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_elts_pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// it's a counter</span></span>

</pre>

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621

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<td class="diff-line-num new_line" data-linenumber="646" style="width: 35px; color: rgba(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="LC646" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="622" 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">

622

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<td class="diff-line-num new_line old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp">    <span class="n" style="color: #333;">priority_queue</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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></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;">greater</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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pq</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// http://stackoverflow.com/questions/2439283/how-can-i-create-min-stl-priority-queue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="623" 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="647" 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="LC647" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// tuple is uf_hash_t, thread_id(=int)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="648" 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">

648

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp">    <span class="n" style="color: #333;">priority_queue</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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></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;">greater</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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pq</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// http://stackoverflow.com/questions/2439283/how-can-i-create-min-stl-priority-queue</span></span>

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<td class="diff-line-num new new_line" data-linenumber="649" 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="LC649" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="650" 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="LC650" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// auxiliary info for threads </span></span>

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623

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</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;">hash_vector_idx</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>

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624

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<td class="diff-line-num new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</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;">hash_vector_size</span><span class="p">(</span><span class="n" style="color: #333;">nb_threads</span><span class="p">);</span></span>

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625

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<td class="diff-line-num new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="632" style="width: 35px; color: rgba(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="660" style="width: 35px; color: rgba(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">@@ -632,11 +660,11 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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632

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<td class="diff-line-num new_line" data-linenumber="660" style="width: 35px; color: rgba(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="LC660" class="line" lang="cpp">            <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">emplace</span><span class="p">(</span><span class="n" style="color: #333;">make_tuple</span><span class="p">(</span><span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">hash_vector_idx</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="p">],</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre>

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633

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661

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="662" style="width: 35px; color: rgba(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="LC662" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="636" 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="663" 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="LC663" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">UINT64_MAX</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">// should be uf_hash_t but let's have it larger to mark a special "prev" initial value </span></span></span>

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<td class="diff-line-num new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="638" 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="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC638" 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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int64</span>_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">elt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">top</span><span class="p">();</span> <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int64</span>_t</span> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">elt</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC666" 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;">tuple</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">u<span class="idiff left right">f_hashes</span>_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">elt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">top</span><span class="p">();</span> <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp">        <span class="n" style="color: #333;">u<span class="idiff left right">f_hashes</span>_t</span> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">elt</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cout << "got " << cur << " queue " << get<1>(elt) << std::endl;</span></span>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">prev</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp">        <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="658" style="width: 35px; color: rgba(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">@@ -658,7 +686,7 @@ void prepare_uf(std::string prefix, IBank *in, const int nb_threads, int& kmerSi</td>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cpp">    <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">uf_hashes_vectors</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="660" style="width: 35px; color: rgba(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="LC688" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line old" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"pass "</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;">pass</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_passes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">nb_elts_pass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" unique hashes written to disk, size "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_elts_pass</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;"><span class="idiff left right">partition</span>_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"pass "</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;">pass</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_passes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">nb_elts_pass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" unique hashes written to disk, size "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_elts_pass</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;"><span class="idiff left right">uf_hashes</span>_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="691" style="width: 35px; color: rgba(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="LC691" class="line" lang="cpp">    <span class="n" style="color: #333;">nb_elts</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nb_elts_pass</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="692" style="width: 35px; color: rgba(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="LC692" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="739" style="width: 35px; color: rgba(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="767" style="width: 35px; color: rgba(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">@@ -739,11 +767,11 @@ void bglue(Storage *storage,</td>

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739

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<td class="diff-line-num new_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

</td>

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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp">        <span class="n" style="color: #333;">prepare_uf</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">nb_prepare_passes</span><span class="p">,</span> <span class="n" style="color: #333;">nb_elts</span><span class="p">,</span> <span class="n" style="color: #333;">nb_glue_sequences</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

<td class="diff-line-num new_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

768

</td>

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

<pre style="margin: 0;"> <span id="LC768" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="diff-line-num new_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

</td>

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

<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// load uf hashes from disk</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="742" 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">

742

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">partition</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uf_hashes</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="770" 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">

770

</td>

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

<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uf_hashes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="diff-line-num new_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

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

<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp">    <span class="n" style="color: #333;">uf_hashes</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">nb_elts</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

</td>

<td class="diff-line-num new_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

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

<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_prepare_passes</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

<td class="diff-line-num new_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

</td>

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

<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="746" 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">

746

</td>

<td class="diff-line-num new_line old" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp">        <span class="n" style="color: #333;">IteratorFile</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int64</span>_t</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;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.hashes."</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;">pass</span><span class="p">));</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="774" 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">

774

</td>

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

<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp">        <span class="n" style="color: #333;">IteratorFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">u<span class="idiff left right">f_hashes</span>_t</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;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.hashes."</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;">pass</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

<td class="diff-line-num new_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

775

</td>

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

<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

<td class="diff-line-num new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

</td>

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

<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp">            <span class="n" style="color: #333;">uf_hashes</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">item</span><span class="p">());</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="diff-line-num new_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

</td>

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

<pre style="margin: 0;"> <span id="LC777" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="751" style="width: 35px; color: rgba(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="779" style="width: 35px; color: rgba(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">@@ -751,12 +779,15 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

</td>

<td class="diff-line-num new_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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

<pre style="margin: 0;"> <span id="LC779" class="line" lang="cpp">        <span class="n" style="color: #333;">uf_hashes</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

</td>

<td class="diff-line-num new_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

</td>

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

<pre style="margin: 0;"> <span id="LC780" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

</td>

<td class="diff-line-num new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

</td>

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

<pre style="margin: 0;"> <span id="LC781" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">nb_uf_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uf_hashes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="754" 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">

754

</td>

<td class="diff-line-num new_line old" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC754" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded all unique UF elements ("</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") into a single vector of size "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">partition</span>_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="782" 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">

782

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

<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded all unique UF elements ("</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") into a single vector of size "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">uf_hashes</span>_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

</td>

<td class="diff-line-num new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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

<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gamma</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// make it even faster.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

<td class="diff-line-num new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

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

<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="758" 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">

758

</td>

<td class="diff-line-num new_line old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// TODO: why not iterate the UF hashes from disk instead of loading them in memory?</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="759" 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">

759

</td>

<td class="diff-line-num new_line old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp">    <span class="n" style="color: #333;">boomphf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mphf</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">partition_t</span> <span class="p">,</span> <span class="cm" style="color: #998; font-style: italic;">/*TODO we don't need hasher_t here now that we're not hashing kmers, but I forgot to change*/</span> <span class="n" style="color: #333;">hasher_t</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">partition_t</span><span class="o" style="font-weight: 600;">></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;">nb_uf_keys</span><span class="p">,</span> <span class="n" style="color: #333;">uf_hashes</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="786" 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">

786

</td>

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

<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// side question:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="787" 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">

787

</td>

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

<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// why not iterate the UF hashes from disk instead of loading them in memory (to construt that mphf)?</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="788" 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">

788

</td>

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

<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// I believe it's because the UF will anyway be loaded in memory after and will also take as much space as those hashes</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="789" 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">

789

</td>

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

<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="790" 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">

790

</td>

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

<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp">    <span class="n" style="color: #333;">boomphf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mphf</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uf_hashes_t</span><span class="p">,</span> <span class="cm" style="color: #998; font-style: italic;">/*TODO we don't need hasher_t here now that we're not hashing kmers, but I forgot to change*/</span> <span class="n" style="color: #333;">hasher_t</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">uf_hashes_t</span><span class="o" style="font-weight: 600;">></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;">nb_uf_keys</span><span class="p">,</span> <span class="n" style="color: #333;">uf_hashes</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

760

</td>

<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

</td>

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

<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

761

</td>

<td class="diff-line-num new_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

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

<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp">    <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">uf_hashes</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

</td>

<td class="diff-line-num new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

</td>

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

<pre style="margin: 0;"> <span id="LC793" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="766" style="width: 35px; color: rgba(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="797" style="width: 35px; color: rgba(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">@@ -766,6 +797,12 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<td class="diff-line-num new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

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<pre style="margin: 0;"> <span id="LC797" class="line" lang="cpp">        <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"UF MPHF constructed ("</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">uf_mphf_memory</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

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<td class="diff-line-num new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

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<pre style="margin: 0;"> <span id="LC798" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

768

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<td class="diff-line-num new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" 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="800" 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="LC800" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span><span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" 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="801" 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">

801

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<pre style="margin: 0;">+<span id="LC801" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" 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="802" 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">

802

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<pre style="margin: 0;">+<span id="LC802" 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;">"cannot create a union-find data structure, too many elements. This should in fact not even happen. Please contact a BCALM 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" 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="803" 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">

803

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp">        <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="769" 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="805" 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">

805

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

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<td class="diff-line-num new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// create a UF data structure</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

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<td class="diff-line-num new_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

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<td class="diff-line-num new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp">    <span class="n" style="color: #333;">unionFind</span> <span class="n" style="color: #333;">ufkmers</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="779" style="width: 35px; color: rgba(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="816" style="width: 35px; color: rgba(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">@@ -779,7 +816,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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<td class="diff-line-num new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

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<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// those were toy one, here is the real one:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

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<td class="diff-line-num new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

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<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// instead of UF of kmers, we do a union find of hashes of kmers. less memory. will have collisions, but that's okay i think. let's see.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="782" 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">

782

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<td class="diff-line-num new_line old" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC782" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// actually, in the current implementation, <span class="idiff left right">partition_t is not used, but values are indeed hardcoded in 32 bits (the UF implementation uses a 64 bits hash table for</span> internal stuff)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" 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="819" 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">

819

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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// actually, in the current implementation, <span class="idiff left right">values are indeed hardcoded in 32 bits (the UF implementation uses a 64 bits hash table but don't get fooled, it's 32 bits of values and 32 bits of</span> internal stuff)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

<td class="diff-line-num new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

<td class="diff-line-num new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We loop over sequences.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

<td class="diff-line-num new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</td>

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

<pre style="margin: 0;"> <span id="LC822" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="875" style="width: 35px; color: rgba(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="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -875,11 +912,12 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

</td>

<td class="diff-line-num new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

912

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<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

876

</td>

<td class="diff-line-num new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

913

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

<pre style="margin: 0;"> <span id="LC913" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

</td>

<td class="diff-line-num new_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

914

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="878" 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">

878

</td>

<td class="diff-line-num new_line old" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC878" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * this is to get rid of the rank (one uint32) per element in the current UF implementation </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="879" 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">

879

</td>

<td class="diff-line-num new_line old" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC879" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * we're using the disk to save space of populating one vector from the other in memory. */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

915

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

<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * this is to get rid of the rank (one uint32) per element in the current UF implementation. </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

916

</td>

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

<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * To do this, we're using the disk to save space of populating one vector from the other in memory. </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

917

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

<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * (saves having to allocate both vectors at the same time) */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

</td>

<td class="diff-line-num new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

918

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

<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="881" 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">

881

</td>

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

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<pre style="margin: 0;">-<span id="LC881" class="line" lang="cpp">    <span class="n" style="color: #333;">BagFile</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left">int64_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bagf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint64</span>_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span>  <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="882" 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">

882

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC882" class="line" lang="cpp">  <span class="n" style="color: #333;">BagCache</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left">int64_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">ufkmers_bag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BagCache</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">uint64</span>_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span>  <span class="n" style="color: #333;">ufkmers_bagf</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span> <span class="p">);</span>   <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">ufkmers_bag</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

919

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

920

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

<td class="diff-line-num new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

921

</td>

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

<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_uf_keys</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

<td class="diff-line-num new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//ufkmers_vector[i] = ufkmers.find(i); // just in-memory without the disk</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="892" style="width: 35px; color: rgba(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="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -892,15 +930,15 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

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<td class="diff-line-num new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

</td>

<td class="diff-line-num new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

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<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp">    <span class="n" style="color: #333;">ufkmers_bag</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

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<td class="diff-line-num new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

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

<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="895" 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">

895

</td>

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

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<pre style="margin: 0;">-<span id="LC895" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left">int32_t</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_vector</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="896" 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">

896

</td>

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

</td>

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<pre style="margin: 0;">-<span id="LC896" class="line" lang="cpp">    <span class="n" style="color: #333;">IteratorFile</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int64</span>_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

933

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

934

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

</td>

<td class="diff-line-num new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

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<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

</td>

<td class="diff-line-num new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

</td>

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

<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

</td>

<td class="diff-line-num new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

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

<pre style="margin: 0;"> <span id="LC937" class="line" lang="cpp">            <span class="n" style="color: #333;">ufkmers_vector</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufkmers_file</span><span class="p">.</span><span class="n" style="color: #333;">item</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

</td>

<td class="diff-line-num new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

</td>

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

<pre style="margin: 0;"> <span id="LC938" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

</td>

<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

</td>

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<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp">    <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue.uf"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

</td>

<td class="diff-line-num new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

</td>

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

<pre style="margin: 0;"> <span id="LC940" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="903" 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">

903

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC903" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded 32-bit UF ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">u<span class="idiff left right">int32</span>_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="941" 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">

941

</td>

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

<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"loaded 32-bit UF ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_uf_keys</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u<span class="idiff left right">f_hashes</span>_t</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" MB)"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

</td>

<td class="diff-line-num new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

</td>

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

<pre style="margin: 0;"> <span id="LC942" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

</td>

<td class="diff-line-num new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

</td>

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<pre style="margin: 0;"> <span id="LC943" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// setup output file</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="diff-line-num new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

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

<pre style="margin: 0;"> <span id="LC944" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">output_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -987,7 +1025,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_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">

987

</td>

<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

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

<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

988

</td>

<td class="diff-line-num new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

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

<pre style="margin: 0;"> <span id="LC1026" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

989

</td>

<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="990" 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">

990

</td>

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

</td>

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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">sum_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sum_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1028" 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">

1028

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

<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">64</span>_t</span> <span class="n" style="color: #333;">sum_abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sum_abundance</span><span class="p">(</span><span class="n" style="color: #333;">abundances</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

</td>

<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1029

</td>

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

</td>

<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

993

</td>

<td class="diff-line-num new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

</td>

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

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1061" style="width: 35px; color: rgba(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="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1061,7 +1099,7 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

</td>

<td class="diff-line-num new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp">            <span class="n" style="color: #333;">outLock</span><span class="p">.</span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1062

</td>

<td class="diff-line-num new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1100

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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1063

</td>

<td class="diff-line-num new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1101

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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="cpp">            <span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">markedSeq</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="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">msInPart</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1064" 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">

1064

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint64</span>_t</span> <span class="n" style="color: #333;">seq_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1102" 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">

1102

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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp">            <span class="n" style="color: #333;"><span class="idiff left right">seq_idx</span>_t</span> <span class="n" style="color: #333;">seq_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1065

</td>

<td class="diff-line-num new_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1103

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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1066

</td>

<td class="diff-line-num new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1104

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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span> <span class="c1" style="color: #998; font-style: italic;">// BankFasta</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1067

</td>

<td class="diff-line-num new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1105

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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1135" style="width: 35px; color: rgba(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">@@ -1097,14 +1135,16 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

</td>

<td class="diff-line-num new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1135

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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp">                <span class="n" style="color: #333;">seq_index</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

<td class="diff-line-num new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1136

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

<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

</td>

<td class="diff-line-num new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

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

<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"></span>

</pre>

</td>

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

1100

</td>

<td class="diff-line-num new_line old" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// now iterates all sequences in a partition to determine the order in which they're going to be glues (avoid intermediate gluing)</span></span>

</pre>

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

1101

</td>

<td class="diff-line-num new_line old" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ordered_sequences_idxs</span> <span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1138" 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">

1138

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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</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;">seq_idx_t</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">seqs_to_glue</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1139" 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">

1139

</td>

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

<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span>              <span class="n" style="color: #333;">seqs_to_glue_is_circular</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1140" 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">

1140

</td>

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

<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1141" 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">

1141

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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// now iterates all sequences in a partition to determine the order in which they're going to be glued</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1102

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<td class="diff-line-num new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msInPart</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;">msInPart</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1103

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<td class="diff-line-num new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1104

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<td class="diff-line-num new_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1144

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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//debug = it->first == 38145; // debug specific partition</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1105

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<td class="diff-line-num new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1145

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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout << "1.processing partition " << it->first << std::endl;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1106" 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">

1106

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<td class="diff-line-num new_line old" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="cpp">                <span class="n" style="color: #333;">determine_order_sequences</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ordered_sequences_idxs</span></span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// return indices of markedSeq's inside it->second</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1107" 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">

1107

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<td class="diff-line-num new_line old" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout << "2.processing partition " << it->first << " nb o<span class="idiff left right">rdered sequences: " << ordered_sequences_idxs</span>.size() << std::endl;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1146" 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">

1146

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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp">                <span class="n" style="color: #333;">determine_order_sequences</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SPAN</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">seqs_to_glue</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">seqs_to_glue_is_circular</span></span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// return indices of markedSeq's inside it->second</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1108" 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="1147" 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">

1147

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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout << "2.processing partition " << it->first << " nb o<span class="idiff left right">f final sequences: " << seqs_to_glue</span>.size() << std::endl;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1108

</td>

<td class="diff-line-num new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1148

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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp">                <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

</td>

<td class="diff-line-num new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1149

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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1110

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<td class="diff-line-num new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1150

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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1125" style="width: 35px; color: rgba(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="1165" style="width: 35px; color: rgba(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">@@ -1125,10 +1165,12 @@ void bglue(Storage *storage,</td>

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1125

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<td class="diff-line-num new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1165

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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="cpp">                <span class="n" style="color: #333;">abundances</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">abundance_str</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

</td>

<td class="diff-line-num new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1127

</td>

<td class="diff-line-num new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

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

<pre style="margin: 0;"> <span id="LC1167" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1128" 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">

1128

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<td class="diff-line-num new_line old" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">itO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ordered_sequences_idxs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itO</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ordered_sequences_idxs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">itO</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1168" 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">

1168

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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span>  <span class="n" style="color: #333;">nb_seqs_to_glue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs_to_glue</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1169" 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">

1169

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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="cpp">            <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">seqs_to_glue_is_circular</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nb_seqs_to_glue</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1170" 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">

1170

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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_seqs_to_glue</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1129

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<td class="diff-line-num new_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1171

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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1130

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<td class="diff-line-num new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="cpp">                <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">abs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1131" 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">

1131

</td>

<td class="diff-line-num new_line old" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="cpp">                <span class="n" style="color: #333;">glue_sequences</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">itO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abundances</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kmerSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</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">// takes as input the indices of ordered sequences, and the markedSeq's themselv</span>es</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

1173

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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="cpp">                <span class="n" style="color: #333;">glue_sequences</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">seqs_to_glue</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs_to_glue_is_circular</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abundances</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kmerSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</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">// takes as input the indices of ordered sequences, whether that sequence is circular, and the markedSeq's themselves along with their abundanc</span>es</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1132

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<td class="diff-line-num new_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1174

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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1133

</td>

<td class="diff-line-num new_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1175

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1134

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<td class="diff-line-num new_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1176

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

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1137" style="width: 35px; color: rgba(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="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1137,7 +1179,8 @@ void bglue(Storage *storage,</td>

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<td class="diff-line-num old_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

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<td class="diff-line-num new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1179

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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1138

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<td class="diff-line-num new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1180

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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1139

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<td class="diff-line-num new_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1181

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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp">                </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1140" 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">

1140

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<td class="diff-line-num new_line old" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1140" 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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1182" 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">

1182

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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="cpp">            <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">seqs_to_glue</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1183" 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">

1183

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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="cpp">            <span class="n" style="color: #333;">free_memory_vector</span><span class="p">(</span><span class="n" style="color: #333;">seqs_to_glue_is_circular</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1141

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<td class="diff-line-num new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1184

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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

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<td class="diff-line-num new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1185

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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp">            <span class="n" style="color: #333;">partitionBank</span><span class="p">.</span><span class="n" style="color: #333;">finalize</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// BankFasta</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

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<td class="diff-line-num new_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1186

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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="13ea1c05cb7d9ae8ed463fc61e80763d1ced17a4">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#13ea1c05cb7d9ae8ed463fc61e80763d1ced17a4"><strong>gatb-core/src/gatb/bcalm2/ograph.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(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="233" style="width: 35px; color: rgba(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">@@ -233,7 +233,7 @@ void graph3<span>::debruijn(){</td>

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<td class="diff-line-num old_line" data-linenumber="233" style="width: 35px; color: rgba(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="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">    <span class="n" style="color: #333;">minusone</span><span class="p">.</span><span class="n" style="color: #333;">setVal</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="234" style="width: 35px; color: rgba(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="234" style="width: 35px; color: rgba(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="LC234" class="line" lang="cpp">  <span class="n" style="color: #333;">left</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">minusone</span><span class="p">,</span> <span class="n" style="color: #333;">SEQ_LEFT</span><span class="p">});</span> <span class="c1" style="color: #998; font-style: italic;">// dummy kmer so that we dont need to check bounds.. clever..</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="235" style="width: 35px; color: rgba(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="LC235" class="line" lang="cpp">  <span class="n" style="color: #333;">right</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">minusone</span><span class="p">,</span> <span class="n" style="color: #333;">SEQ_LEFT</span><span class="p">});</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="236" 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="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp">    <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">debug_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="237" 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="236" 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="LC236" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>uint debug_index = 0;</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="238" style="width: 35px; color: rgba(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="238" style="width: 35px; color: rgba(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="LC238" 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;">indiceUnitigs</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,7 +255,7 @@ void graph3<span>::debruijn(){</td>

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<td class="diff-line-num old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//~ if (debug_index > 0) if (kL.indice == debug_index || kR.indice == debug_index ) std::cout << " identical, kl / kR " << kL.indice << " " << kR.indice << " unitigs " << unitigs[kL.indice] << " " << unitigs[kR.indice] << " positions "  << kL.position << " " << kR.position << std::endl;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//~ if(isNumber (unitigs[kL.indice][0])){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">//~ }</span></span>

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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kL</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span>=</span><span class="n" style="color: #333;">kR</span><span class="p">.</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">kL</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">!</span>=</span><span class="n" style="color: #333;">kR</span><span class="p">.</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp">                          <span class="n" style="color: #333;">update_connected</span><span class="p">(</span><span class="n" style="color: #333;">kL</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp">                          <span class="n" style="color: #333;">update_connected</span><span class="p">(</span><span class="n" style="color: #333;">kR</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp">                  <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -265,7 +265,7 @@ void graph3<span>::debruijn(){</td>

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<td class="diff-line-num old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp">                  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iL</span><span class="p">;</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iR</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">].</span><span class="n" style="color: #333;">kmmer</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">kL</span><span class="p">.</span><span class="n" style="color: #333;">kmmer</span><span class="p">){</span></span>

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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(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="LC267" class="line" lang="cpp">                          <span class="n" style="color: #333;">go</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">left</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iL</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span>=</span><span class="n" style="color: #333;">right</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">].</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">left</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iL</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">!</span>=</span><span class="n" style="color: #333;">right</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">].</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="269" style="width: 35px; color: rgba(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="LC269" class="line" lang="cpp">                                  <span class="n" style="color: #333;">update_connected</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">[</span><span class="n" style="color: #333;">iL</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(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="LC270" class="line" lang="cpp">                          <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(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="LC271" class="line" lang="cpp">                          <span class="c1" style="color: #998; font-style: italic;">//~ while(left[++iL].kmmer<=kR.kmmer ){}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -277,7 +277,7 @@ void graph3<span>::debruijn(){</td>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp">                  <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(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="LC278" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">right</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="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">kL</span><span class="p">.</span><span class="n" style="color: #333;">kmmer</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp">                          <span class="n" style="color: #333;">go</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">left</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iL</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span>=</span><span class="n" style="color: #333;">right</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">].</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">left</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iL</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">indice</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">!</span>=</span><span class="n" style="color: #333;">right</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">].</span><span class="n" style="color: #333;">indice</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp">                                  <span class="n" style="color: #333;">update_connected</span><span class="p">(</span><span class="n" style="color: #333;">right</span><span class="p">[</span><span class="n" style="color: #333;">iR</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">                          <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp">                          <span class="c1" style="color: #998; font-style: italic;">//~ while(right[++iR].kmmer<=kL.kmmer ){}</span></span>

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<li id="a434192ac5c383bb512502817a95c4f4cc9378dc">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#a434192ac5c383bb512502817a95c4f4cc9378dc"><strong>gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.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">@@ -151,8 +151,8 @@ struct FunctorNodes</td>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()</span> <span class="p">(</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">node</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We get branching nodes neighbors for the current node.</span></span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp">        <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">successors</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;"><span class="idiff left">template</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">successors</span>   <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp">        <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">predecessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;"><span class="idiff left">template</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">predecessors</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp">        <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">successors</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">successors</span>   <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp">        <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">predecessors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">predecessors</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="p">(</span><span class="n" style="color: #333;">successors</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;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">predecessors</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;">1</span><span class="p">)</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp">        <span class="p">{</span></span>

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<li id="2ff315124cb4ed9eebb9d35c35743144de29a781">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#2ff315124cb4ed9eebb9d35c35743144de29a781"><strong>gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="888" style="width: 35px; color: rgba(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="888" style="width: 35px; color: rgba(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">@@ -888,7 +888,9 @@ GraphUnitigsTemplate<span>::GraphUnitigsTemplate (tools::misc::IProperties* para</td>

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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We create a storage instance. */</span></span>

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<pre style="margin: 0;"> <span id="LC889" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/* (this is actually loading, not creating, the storage at "uri") */</span></span>

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<pre style="margin: 0;"> <span id="LC890" class="line" lang="cpp">        <span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_storageMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_from_hdf5</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">STORAGE_HDF5</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">STORAGE_FILE</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC891" class="line" lang="cpp">        <span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setStorage</span> <span class="p">(</span><span class="n" style="color: #333;">StorageFactory</span><span class="p">(</span><span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_storageMode</span><span class="p">).</span><span class="n" style="color: #333;">create</span> <span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">append</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// in principle we wouldn't need to modify the .h5 file when building unitigs, but at some very rare locations in the code, we do (like nb_unitigs)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp">        <span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setStorage</span> <span class="p">(</span><span class="n" style="color: #333;">StorageFactory</span><span class="p">(</span><span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_storageMode</span><span class="p">).</span><span class="n" style="color: #333;">create</span> <span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">append</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC895" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We get some properties. */</span></span>

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="cpp">        <span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_state</span>     <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">GraphUnitigsTemplate</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;">StateMask</span><span class="p">)</span> <span class="n" style="color: #333;">atol</span> <span class="p">(</span><span class="n" style="color: #333;">BaseGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getGroup</span><span class="p">().</span><span class="n" style="color: #333;">getProperty</span> <span class="p">(</span><span class="s" style="color: #d14;">"state"</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1742" style="width: 35px; color: rgba(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">@@ -1742,6 +1744,10 @@ simplePathLongest_avance(const NodeGU& node, Direction dir, int& seqLength, int&</td>

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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="cpp">        <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">EdgeGU</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">in_neighbors_vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">neighborsEdge</span> <span class="p">(</span><span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">dir</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC1745" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">in_neighbors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_neighbors_vec</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="LC1746" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC1748" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_neighbors</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="LC1749" 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;">"simplePathLongest_avance stopped at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">cur_node</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" because of surprising lack of in-neighbor given that we had to come from somewhere"</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="LC1750" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">in_neighbors</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="LC1752" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We check we have no in-branching. */</span></span>

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<pre style="margin: 0;"> <span id="LC1753" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_neighbors</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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<br>

</li>

<li id="a57dcb64f25d9850b62e0fd29229dc775bc27187">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#a57dcb64f25d9850b62e0fd29229dc775bc27187"><strong>gatb-core/src/gatb/debruijn/impl/IterativeExtensions.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">@@ -80,7 +80,7 @@ struct NodeDepth</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Node</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Edge</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">IterativeExtensions</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="n" style="color: #333;">Node</span><span class="p">,</span> <span class="n" style="color: #333;">Edge</span><span class="p">,</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">compare_and_mark_last_k_minus_one_mer</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;">node</span><span class="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">kmer_type</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">kmers_set</span><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="n" style="color: #333;">KmerModel</span> <span class="n" style="color: #333;">leftKmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">.</span><span class="n" style="color: #333;">codeSeed</span> <span class="p">(</span><span class="n" style="color: #333;">node</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 class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">    <span class="n" style="color: #333;">KmerModel<span class="idiff left right">Direct</span></span> <span class="n" style="color: #333;">leftKmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">.</span><span class="n" style="color: #333;">codeSeed</span> <span class="p">(</span><span class="n" style="color: #333;">node</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 class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">    <span class="n" style="color: #333;">kmer_type</span> <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leftKmer</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kmers_set</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kmers_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -115,7 +115,7 @@ IterativeExtensions<span, Node, Edge, Graph>::IterativeExtensions (</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">      <span class="n" style="color: #333;">max_depth</span><span class="p">(</span><span class="n" style="color: #333;">max_depth</span><span class="p">),</span> <span class="n" style="color: #333;">max_nodes</span><span class="p">(</span><span class="n" style="color: #333;">max_nodes</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><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;">model</span>         <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">()</span>  <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp">    <span class="n" style="color: #333;">modelMinusOne</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp">    <span class="n" style="color: #333;">modelMinusOne</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Model<span class="idiff left right">Direct</span></span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(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">@@ -168,7 +168,7 @@ void IterativeExtensions<span, Node, Edge, Graph>::construct_linear_seqs (</td>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef DONTMARK</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">kmer_type</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">already_extended_from</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//   compare_and_mark_last_k_minus_one_mer(L, already_extended_from); // mark first kmer to never extend from it again, // L will be marked at first iteration below</span></span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left">compare_and_mark_last_k_minus_one_mer</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">L</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">already_extended_from</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">// mark first kmer to never extend from it again</span></span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We will need a Path object and a Sequence object during the extension. */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(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">@@ -271,12 +271,14 @@ void IterativeExtensions<span, Node, Edge, Graph>::construct_linear_seqs (</td>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef DONTMARK</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// make sure this is the only time we see this (k-1)-overlap</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">already_seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compare_and_mark_last_k_minus_one_mer</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">ksd</span><span class="p">.</span><span class="n" style="color: #333;">node</span><span class="p">),</span> <span class="n" style="color: #333;">already_extended_from</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">already_seen</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp">            <span class="n" style="color: #333;">INFO</span> <span class="p">((</span><span class="s" style="color: #d14;">"... XXX not extending node %s becaues last k-1-mer was already seen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">toString</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="LC279" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">len_right</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span>  <span class="c1" style="color: #998; font-style: italic;">//==0 particular case of the first contig, contig already marked (before the loop), do not mark again, this will stop extension</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// make sure this is the only time we see this (k-1)-overlap (end of the just built contig)</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">already_seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compare_and_mark_last_k_minus_one_mer</span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">endNode</span><span class="p">),</span> <span class="n" style="color: #333;">already_extended_from</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">already_seen</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">                <span class="n" style="color: #333;">INFO</span> <span class="p">((</span><span class="s" style="color: #d14;">"... XXX not extending node %s becaues last k-1-mer was already seen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="281" 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="LC281" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"></span>

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<li id="c8b46ef3dbdf675bf383053ecb5973e97e8abe00">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#c8b46ef3dbdf675bf383053ecb5973e97e8abe00"><strong>gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(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">@@ -46,6 +46,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** ShortcutS. */</span></span>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelCanonical</span>       <span class="n" style="color: #333;">Model</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelCanonical</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span> <span class="n" style="color: #333;">KmerModel</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="49" 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="LC49" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelDirect</span>       <span class="n" style="color: #333;">ModelDirect</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="49" 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="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelDirect</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span> <span class="n" style="color: #333;">KmerModelDirect</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;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span>                 <span class="n" style="color: #333;">kmer_type</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(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="LC52" class="line" lang="cpp"></span>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,7 +111,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span>                             <span class="n" style="color: #333;">max_nodes</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp">    <span class="n" style="color: #333;">Model</span> <span class="n" style="color: #333;">model</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp">    <span class="n" style="color: #333;">Model</span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="cpp">    <span class="n" style="color: #333;">Model<span class="idiff left right">Direct</span></span> <span class="n" style="color: #333;">modelMinusOne</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Fill a Sequence instance from the results of the current graph traversal.</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] node : starting node of the path</span></span>

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</li>

<li id="34ae9ab374303a1000194fa7d58aeba9d58f32ce">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#34ae9ab374303a1000194fa7d58aeba9d58f32ce"><strong>gatb-core/src/gatb/debruijn/impl/LinkTigs.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">@@ -30,7 +30,7 @@ using namespace gatb::core::system::impl;</td>

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<pre style="margin: 0;"> <span id="LC30" 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;">core</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">debruijn</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">impl</span>  <span class="p">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_passes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_final_output</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;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_final_output</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;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">renumber_unitigs</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">get_link_from_file</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;">ifstream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">link</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">unitig_id</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* this procedure finds the overlaps between unitigs, using a hash table of all extremity (k-1)-mers</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">@@ -42,30 +42,68 @@ namespace gatb { namespace core { namespace debruijn { namespace impl  {</td>

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<pre style="margin: 0;"> <span id="LC42" 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="LC43" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * so the memory usage is just that of the hash tables that record kmers, not of the links</span></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="cm" style="color: #998; font-style: italic;"> * Assumption: FASTA header of unitigs starts with a unique number (unitig ID). </span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Normally bcalm outputs consecutive unitig ID's but LinkTigs could also work with non-consecutive, non-sorted IDs</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  Two modes of operation:</span></span>

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<pre style="margin: 0;">+<span id="LC46" 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="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  renumber_unitigs == true: FASTA header can be anything. Useful for any program that has removed some unitigs, e.g. merci.</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  LinkTigs will take the header and split it into space-separated fields, remove the first field and keep the remaining ones.</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  The first field will be replaced by numbered IDs in consecutive order, between 0 and |nb_unitigs|-1. </span></span>

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<pre style="margin: 0;">+<span id="LC50" 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="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *  renumber_unitigs == false: then FASTA headers of unitigs _needs_ to start with a unique number (unitig ID). </span></span>

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

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_tigs</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_tigs</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">renumber_unitigs</span></span><span class="p">)</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankFasta</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".<span class="idiff left right">index</span>ed"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error, <span class="idiff left right">recent optimizations (specifically link_unitigs) don't support k<5 for now</span>"</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="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="58" 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="LC58" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankFasta</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".<span class="idiff left right">link</span>ed"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="59" 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">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error, <span class="idiff left right">link_unitigs doesn't support k<5, sorry. Contact a developer if you really need k<4 support (alternatively: construct that tiny dBG using Python :)</span>"</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="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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">

57

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

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp">        <span class="n" style="color: #333;">link_unitigs_pass</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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

<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line old" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp">    <span class="n" style="color: #333;">write_final_output</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="60" 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="65" 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="LC65" class="line" lang="cpp">    <span class="n" style="color: #333;">write_final_output</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">nb_unitigs</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">renumber_unitigs</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">    <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">);</span></span>

</pre>

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

63

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<td class="diff-line-num new_line old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp">    <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">rename</span> <span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".<span class="idiff left right">index</span>ed"</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="69" 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">

69

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

<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">    <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">rename</span> <span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".<span class="idiff left right">link</span>ed"</span><span class="p">,</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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

<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"Done finding links between unitigs"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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

<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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

<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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

<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="69" 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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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

<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* strip L:'s from a comment line*/</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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

<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">remove_previous_links</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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

<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" 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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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

<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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

<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"parsing unitig links for "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" 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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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

<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">   <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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

<pre style="margin: 0;">+<span id="LC81" 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;">stringstream</span> <span class="n" style="color: #333;">stream</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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

<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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

<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tok</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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

<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">        <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">tok</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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

<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">stream</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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

<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="87" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="69" 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="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tok</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

</td>

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

<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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

<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"L:"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="91" 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">

91

</td>

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

<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="92" 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">

92

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

<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">                   <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tok</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="93" 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">

93

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

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

94

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

<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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;">//res =  res.substr(0,res.size()-2);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"returning "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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

<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

98

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

<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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

<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* keep all the comment line except the first field*/</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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

<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">strip_first_field</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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

<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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

<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

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

<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

105

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

<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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

<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * takes all the prefix.links.* files, sorted by unitigs.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * do a n-way merge to gather the links for each unitig in unitig order</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +111,7 @@ void link_tigs(string unitigs_filename, int kmerSize, int nb_threads, uint64_t &</td>

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(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="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_final_output</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;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write_final_output</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;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">renumber_unitigs</span></span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(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="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"gathering links from disk"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(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="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="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;">ifstream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inputLinks</span><span class="p">[</span><span class="n" style="color: #333;">nb_passes</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(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="126" style="width: 35px; color: rgba(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">@@ -88,7 +126,8 @@ static void write_final_output(const string& unitigs_filename, bool verbose, Ban</td>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(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="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">cur_links</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">comment</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" class="line" lang="cpp">    <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">toString</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">    <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComment</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" 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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" 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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">  <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_previous_links</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" 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="130" 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="LC130" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

131

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_passes</span><span class="p">;</span> <span class="n" style="color: #333;">pass</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">link</span><span class="p">;</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">unitig</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(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">@@ -102,6 +141,10 @@ static void write_final_output(const string& unitigs_filename, bool verbose, Ban</td>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">last_unitig</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">    <span class="n" style="color: #333;">nb_unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// passed variable</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">first_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span> </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="146" 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">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">        <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strip_first_field</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="cpp"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(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="LC148" class="line" lang="cpp"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// nb_passes-way merge sort</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">finished</span><span class="p">.</span><span class="n" style="color: #333;">all</span><span class="p">())</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,6 +153,12 @@ static void write_final_output(const string& unitigs_filename, bool verbose, Ban</td>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">unitig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_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">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_one</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// handles the case where first unitig isn't labeled 0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="cpp">            <span class="n" style="color: #333;">last_unitig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unitig</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">            <span class="n" style="color: #333;">first_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="161" 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="LC161" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(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="162" style="width: 35px; color: rgba(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="LC162" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unitig</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">last_unitig</span><span class="p">)</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="cpp">            <span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">s</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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(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="172" style="width: 35px; color: rgba(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">@@ -123,6 +172,9 @@ static void write_final_output(const string& unitigs_filename, bool verbose, Ban</td>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">            <span class="n" style="color: #333;">itSeq</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="cpp">            <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">toString</span><span class="p">();</span></span>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(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="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="cpp">            <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComment</span><span class="p">();</span></span>

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<td class="diff-line-num new old_line" data-linenumber="126" 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="175" 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="LC175" class="line" lang="cpp">          <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remove_previous_links</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" 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="176" 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="LC176" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" 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="177" 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="LC177" class="line" lang="cpp">                <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_unitigs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strip_first_field</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(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="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp">            </span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp">        <span class="n" style="color: #333;">cur_links</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">get</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,12 +265,13 @@ static void record_links(uint64_t utig_id, int pass, const string &link, std::of</td>

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

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

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

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">link_unitigs_pass</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">unitigs_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">)</span></span>

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

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

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<td class="diff-line-num old_line" data-linenumber="218" style="width: 35px; color: rgba(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="LC270" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">ModelCanonical</span> <span class="n" style="color: #333;">Model</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="219" style="width: 35px; color: rgba(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="LC271" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">kmer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span>           <span class="n" style="color: #333;">Type</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="222" 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="LC274" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">utig_counter</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="LC275" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span> <span class="n" style="color: #333;">inputBank</span> <span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span> <span class="n" style="color: #333;">itSeq</span> <span class="p">(</span><span class="n" style="color: #333;">inputBank</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,6 +292,8 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">        <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;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComment</span><span class="p">();</span>        </span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">utig_id</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;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span> <span class="n" style="color: #333;">utig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utig_counter</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp">        </span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_in_pass</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">UNITIG_BEGIN</span><span class="p">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">        <span class="p">{</span> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="312" style="width: 35px; color: rgba(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">@@ -257,6 +312,8 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp">            <span class="n" style="color: #333;">utigs_links_map</span><span class="p">[</span><span class="n" style="color: #333;">kmerEnd</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">()].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">eEnd</span><span class="p">.</span><span class="n" style="color: #333;">pack</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// there is no UNITIG_BOTH here because we're taking (k-1)-mers.</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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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">        <span class="n" style="color: #333;">utig_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC319" 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;">links_file</span><span class="p">(</span><span class="n" style="color: #333;">unitigs_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".links."</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;">pass</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(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="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -264,6 +321,9 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_hashed_entries</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="LC322" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">utigs_links_map</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp">        <span class="n" style="color: #333;">nb_hashed_entries</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> </span>

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<td class="diff-line-num new old_line" data-linenumber="267" 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="LC324" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="267" 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="LC325" class="line" lang="cpp">    <span class="n" style="color: #333;">utig_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="267" 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="LC326" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp">    <span class="n" style="color: #333;">logging</span><span class="p">(</span><span class="s" style="color: #d14;">"step 2 ("</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;">utigs_links_map</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;">"kmers/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_hashed_entries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"extremities)"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">itSeq</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">itSeq</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">itSeq</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(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">@@ -271,6 +331,8 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp">        <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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">toString</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">        <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;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComment</span><span class="p">();</span>        </span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">utig_id</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;">stoul</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">comment</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp">        </span>

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<td class="diff-line-num new new_line" data-linenumber="335" 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="LC335" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">renumber_unitigs</span><span class="p">)</span> <span class="n" style="color: #333;">utig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">utig_counter</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="336" style="width: 35px; color: rgba(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="LC336" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"unitig "</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">utig_id</span><span class="p">)</span>  <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" : "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seq</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="LC338" class="line" lang="cpp"> </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="440" style="width: 35px; color: rgba(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">@@ -378,6 +440,8 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa</td>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp">            <span class="n" style="color: #333;">record_links</span><span class="p">(</span><span class="n" style="color: #333;">utig_id</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">out_links</span><span class="p">,</span> <span class="n" style="color: #333;">links_file</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp">        <span class="n" style="color: #333;">utig_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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

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

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

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<br>

</li>

<li id="8d46876b0b01c8687ffec95a3e56a84f1d5ffc83">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#8d46876b0b01c8687ffec95a3e56a84f1d5ffc83"><strong>gatb-core/src/gatb/debruijn/impl/LinkTigs.hpp</strong></a>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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<br>

</li>

<li id="3d59b6581d3871516a6b55261db0dac87fd2a525">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#3d59b6581d3871516a6b55261db0dac87fd2a525"><strong>gatb-core/src/gatb/debruijn/impl/Simplifications.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1108" style="width: 35px; color: rgba(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="1108" style="width: 35px; color: rgba(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">@@ -1108,7 +1108,8 @@ void Simplifications<GraphType,Node,Edge>::heuristic_most_covered_path_unitigs(</td>

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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="cpp">            <span class="n" style="color: #333;">current_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">neighbors</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">to</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_graph</span><span class="p">.</span><span class="n" style="color: #333;">degree</span><span class="p">(</span><span class="n" style="color: #333;">current_node</span><span class="p">,</span> <span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">dir</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC1111" 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;">"Weird, there was supposed to be an in-neighbor. Maybe there's a loop. Remove this print if it never happens"</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="LC1111" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// actually this happens for kmers that are linked to themselves (e.g. k=5, AAATT, is connected to its own revcomp AATTT, so it's fine to end the simple path here on those cases)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//std::cout << "Weird, there was supposed to be an in-neighbor. Maybe there's a loop. Remove this print if it never happens" << "in degree " << _graph.degree(current_node, reverse(dir)) << " node" <<  _graph.toString(current_node)  << std::endl;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="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>

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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">@@ -1280,7 +1281,7 @@ unsigned long Simplifications<GraphType,Node,Edge>::removeBulges()</td>

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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <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;">_graph</span><span class="p">.</span><span class="n" style="color: #333;">getKmerSize</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxBulgeLength</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;">max</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_bulgeLen_kMult</span><span class="p">),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_bulgeLen_kAdd</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// SPAdes, exactly</span></span>

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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">backtrackingLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">_bulgeAltPath_kAdd</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//maxBulgeLength; // arbitrary, but if too high it will take much time; // with unitigs, no reason that it has to depend on k, but for some reason, setting it to just "k" doesnt remove nearly as many bulges as k=20. todo investigate that someday.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1283" 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="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1283" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">altPathCovMult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_bulgeAltPath_covMult</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1284" 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="1284" 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="LC1284" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff right">      </span> <span class="n" style="color: #333;">altPathCovMult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_bulgeAltPath_covMult</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// stats</span></span>

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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//</span></span>

</pre>

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<br>

</li>

<li id="b5330caa1a1248a1b6246d8caa9f656b0e8218c1">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#b5330caa1a1248a1b6246d8caa9f656b0e8218c1"><strong>gatb-core/src/gatb/debruijn/impl/Simplifications.hpp</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +66,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span>       <span class="n" style="color: #333;">_bulgeLen_kMult</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_bulgeAltPath_kAdd</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span> <span class="n" style="color: #333;">_bulgeAltPath_covMult</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="70" 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="69" 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="LC69" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff right">      </span> <span class="n" style="color: #333;">_bulgeAltPath_covMult</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">_ecLen_kMult</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">_ecRCTCcutoff</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="4dce1e5207210c91bde58be44fc7ca206c6fa1e7">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#4dce1e5207210c91bde58be44fc7ca206c6fa1e7"><strong>gatb-core/src/gatb/debruijn/impl/Terminator.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">@@ -46,7 +46,7 @@ BranchingTerminatorTemplate<Node,Edge,Graph>::BranchingTerminatorTemplate (const</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">TerminatorTemplate</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="p">,</span><span class="n" style="color: #333;">Edge</span><span class="p">,</span><span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We loop over the branching nodes. */</span></span>

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<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">    <span class="n" style="color: #333;">GraphIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchingNode_t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itBranching</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_graph</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">Graph</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="k" style="font-weight: 600;"><span class="idiff">template</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">iteratorBranching</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    <span class="n" style="color: #333;">GraphIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BranchingNode_t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Node</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">itBranching</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_graph</span><span class="p">.</span><span class="n" style="color: #333;">iteratorBranching</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;">for</span> <span class="p">(</span><span class="n" style="color: #333;">itBranching</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">itBranching</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">itBranching</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We add the current branching node into the map. */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(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">@@ -196,7 +196,7 @@ void BranchingTerminatorTemplate<Node,Edge,Graph>::mark (Node& node)</td>

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

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We loop the neighbors edges of the current node. */</span></span>

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<td class="diff-line-num new_line old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp">    <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">neighbors</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_graph</span><span class="p">.</span><span class="k" style="font-weight: 600;"><span class="idiff left">template</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">neighborsEdge</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">kmer</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp">    <span class="n" style="color: #333;">GraphVector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Edge</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">neighbors</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_graph</span><span class="p">.</span><span class="n" style="color: #333;">neighborsEdge</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">kmer</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(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="201" style="width: 35px; color: rgba(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="LC201" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We loop the branching neighbors. */</span></span>

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<pre style="margin: 0;"> <span id="LC202" 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;">size_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;">neighbors</span><span class="p">.</span><span class="n" style="color: #333;">size</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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<li id="1585bdf1cfb187c932725cb3cea90f0f3a5efa7e">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#1585bdf1cfb187c932725cb3cea90f0f3a5efa7e"><strong>gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -252,10 +252,17 @@ void ConfigurationAlgorithm<span>::execute ()</td>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We get some information about the bank. */</span></span>

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<td class="diff-line-num old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp">    <span class="n" style="color: #333;">_bank</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">estimate</span> <span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_estimateSeqNb</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_estimateSeqTotalSize</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_estimateSeqMaxSize</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//printf("_estimateSeqNb %llu _estimateSeqTotalSize %llu _estimateSeqMaxSize %llu \n", _config._estimateSeqNb, _config._estimateSeqTotalSize, _config._estimateSeqMaxSize);</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(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="LC258" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We get the number of sub banks. */</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp">    <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_banks</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;">getCompositionNb</span><span class="p">();</span></span>

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

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<td class="diff-line-num new old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_banks</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="LC262" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">          <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We memorize the number of abundance min values set by the user.</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * Note that it can be lower than the number of banks. */</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">    <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_abundanceUserNb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_abundance</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -311,11 +318,14 @@ void ConfigurationAlgorithm<span>::execute ()</td>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp">    <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_volume</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_kmersNb</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;">Type</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">MBYTE</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// in MBytes</span></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="314" 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="321" 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="LC321" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//printf("estimated usedSeqLen %llu _estimateSeqNb %llu _kmersNb %llu  _volume %llu  \n", usedSeqLen, _config._estimateSeqNb, kmersNb, _config._volume);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="314" 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="322" 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="LC322" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_volume</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="p">{</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_volume</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span>    <span class="c1" style="color: #998; font-style: italic;">// tiny files fix</span></span>

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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(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="324" style="width: 35px; color: rgba(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="LC324" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="316" style="width: 35px; color: rgba(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="325" style="width: 35px; color: rgba(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="LC325" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">volume_minim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_volume</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">1.2</span>  <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//0.5 for using kxmers   1.2 if bad repartition of minimizers ( todo sampling to assert ram usage)</span></span>

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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(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="LC326" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="318" style="width: 35px; color: rgba(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="327" style="width: 35px; color: rgba(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="LC327" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">volume_minim</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="p">{</span> <span class="n" style="color: #333;">volume_minim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span>    <span class="c1" style="color: #998; font-style: italic;">// tiny files fix</span></span>

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<td class="diff-line-num new old_line" data-linenumber="319" 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="328" 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="LC328" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// volume_minim is used a bit later</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="320" style="width: 35px; color: rgba(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="LC330" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We get max(75%, 100% - X GB) */</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_max_disk_space</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_max_disk_space</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;">max</span> <span class="p">((</span><span class="mi" style="color: #099;">75</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_available_space</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_available_space</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">available_space_min</span><span class="p">);</span>  <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="341" style="width: 35px; color: rgba(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="351" style="width: 35px; color: rgba(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">@@ -341,7 +351,7 @@ void ConfigurationAlgorithm<span>::execute ()</td>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//_nb_passes = 1; //do not constrain nb passes on disk space anymore (anyway with minim, not very big)</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//increase it only if ram issue</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//printf("_volume  %lli volume_minim %lli _max_disk_space %lli  _nb_passes init %i  \n", _<span class="idiff left right">volume,volume_minim,_max_disk_space,</span>_nb_passes);</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//printf("_volume  %lli volume_minim %lli _max_disk_space %lli  _nb_passes init %i  \n", _<span class="idiff left right">config._volume,volume_minim, _config._max_disk_space, _config.</span>_nb_passes);</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_open_files</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;">getMaxFilesNumber</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"></span>

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<li id="7026e2876c610bcf71aa5114af58599b6d8a4f13">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#7026e2876c610bcf71aa5114af58599b6d8a4f13"><strong>gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" style="width: 35px; color: rgba(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="337" style="width: 35px; color: rgba(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">@@ -337,6 +337,9 @@ void DebloomAlgorithm<span>::execute_aux (</td>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** We may have reach the maximum number of items in the partition. */</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">partition</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">partition</span><span class="p">.</span><span class="n" style="color: #333;">getMaxNbItems</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">                          <span class="c1" style="color: #998; font-style: italic;">//first erase the destination file because BagFile creator does not erase previous file anymore</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">                          <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">outputUri</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp">                          </span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">                <span class="cm" style="color: #998; font-style: italic;">/** We exclude the partition content from the critical false positive file. */</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">                <span class="n" style="color: #333;">end_debloom_partition</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp">                    <span class="n" style="color: #333;">partition</span><span class="p">,</span></span>

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<li id="a8c2c0b48f4fe5a6db4d07e69030b1be23067359">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#a8c2c0b48f4fe5a6db4d07e69030b1be23067359"><strong>gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -249,17 +249,22 @@ void MPHFAlgorithm<span,Abundance_t,NodeState_t>::populate ()</td>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We get the abundance of the current kmer. */</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itKmers</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">item</span><span class="p">().</span><span class="n" style="color: #333;">abundance</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_abundance_discrete</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp">            <span class="n" style="color: #333;">_nb_abundances_above_precision</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//std::cout << "found abundance larger than discrete: " << abundance << std::endl;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp">            <span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_abundance_discrete</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idx</span> <span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_abundance_discrete</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">                  <span class="n" style="color: #333;">_nb_abundances_above_precision</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">//std::cout << "found abundance larger than discrete: " << abundance << std::endl;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">                  <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_abundanceDiscretization</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;">2</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="260" 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="LC260" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">          <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">//get first cell strictly greater than abundance</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">                  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span>  <span class="n" style="color: #333;">up</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;">upper_bound</span><span class="p">(</span><span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">abundance</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">                  <span class="n" style="color: #333;">up</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// get previous cell</span></span>

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<td class="diff-line-num new old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">                  <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">up</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="259" 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="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//get first cell strictly greater than abundance</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span>  <span class="n" style="color: #333;">up</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;">upper_bound</span><span class="p">(</span><span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">abundance</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp">          <span class="n" style="color: #333;">up</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// get previous cell</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="262" 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="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">up</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We set the abundance of the current kmer. */</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp">        <span class="n" style="color: #333;">_abundanceMap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>

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</li>

<li id="594afd8796d14815b648e15a5aa082a670521b57">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#594afd8796d14815b648e15a5aa082a670521b57"><strong>gatb-core/src/gatb/kmer/impl/Model.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1434" style="width: 35px; color: rgba(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="1434" style="width: 35px; color: rgba(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">@@ -1434,7 +1434,7 @@ struct Kmer</td>

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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="cpp"></span>

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1435

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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">//reste du newbyte avec le superk</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1436" style="width: 35px; color: rgba(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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1436

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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC1437" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">skid</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="LC1437" class="line" lang="cpp">                 <span class="n" style="color: #333;"><span class="idiff left right">u</span>int</span> <span class="n" style="color: #333;">skid</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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1438

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1438

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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="cpp">                 </span>

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1439

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<pre style="margin: 0;"> <span id="LC1439" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span></span>

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1440

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1440

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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="cpp">                 <span class="p">{</span></span>

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<br>

</li>

<li id="c96a868ed336609b4f21c39702ce23f33c3e7850">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#c96a868ed336609b4f21c39702ce23f33c3e7850"><strong>gatb-core/src/gatb/kmer/impl/PartiInfo.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(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">@@ -24,7 +24,9 @@</td>

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<pre style="margin: 0;"> <span id="LC24" 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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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define DEBUG(a) //printf a</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// wanted to debug separately, DEBUG has more output than debug2</span></span>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// wanted to debug things separately:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// now there are many different and mutually exclusive debug messages</span></span>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// DEBUG has more output than debug2</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC30" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// to see top20 repartitions of bins, uncomment IFDEBUG and DEBUG2</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(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="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define IFDEBUG(a)  //a</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;">#define DEBUG2(a) //printf a</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="229" style="width: 35px; color: rgba(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="231" style="width: 35px; color: rgba(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">@@ -229,12 +231,11 @@ void Repartitor::load (tools::storage::impl::Group& group)</td>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" 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;">storage</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;">Storage</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="n" style="color: #333;">is</span> <span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="s" style="color: #d14;">"minimRepart"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">    <span class="n" style="color: #333;">is</span><span class="p">.</span><span class="n" style="color: #333;">read</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span>     <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">is</span><span class="p">.</span><span class="n" style="color: #333;">read</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_mm</span><span class="p">,</span>         <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_mm</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp">    <span class="n" style="color: #333;">is</span><span class="p">.</span><span class="n" style="color: #333;">read</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nb_minims</span><span class="p">,</span>  <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nb_minims</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">    <span class="n" style="color: #333;">is</span><span class="p">.</span><span class="n" style="color: #333;">read</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nbPass</span><span class="p">,</span>     <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nbPass</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="s" style="color: #d14;">"[Repartitor::load] :  _nbpart=%d  _<span class="idiff left right">mm=%d  _</span>nb_minims=%d  _nbPass=%d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="n" style="color: #333;">_<span class="idiff left">mm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>nb_minims</span><span class="p">,</span> <span class="n" style="color: #333;">_nbPass</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="s" style="color: #d14;">"[Repartitor::load] :  _nbpart=%d  _nb_minims=%d  _nbPass=%d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_minims</span><span class="p">,</span> <span class="n" style="color: #333;">_nbPass</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** We allocate a table whose size is the number of possible minimizers. */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" style="width: 35px; color: rgba(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">@@ -269,15 +270,14 @@ void Repartitor::load (tools::storage::impl::Group& group)</td>

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<pre style="margin: 0;"> <span id="LC270" 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="LC271" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Repartitor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">save</span> <span class="p">(</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">storage</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;">Group</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="s" style="color: #d14;">"[Repartitor::save] :  _nbpart=%d  _<span class="idiff left right">mm=%d  _</span>nb_minims=%d  _nbPass=%d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="n" style="color: #333;">_<span class="idiff left">mm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>nb_minims</span><span class="p">,</span> <span class="n" style="color: #333;">_nbPass</span></span>

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<td class="diff-line-num new new_line" data-linenumber="273" 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="LC273" class="line" lang="cpp">    <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="s" style="color: #d14;">"[Repartitor::save] :  _nbpart=%d  _nb_minims=%d  _nbPass=%d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_minims</span><span class="p">,</span> <span class="n" style="color: #333;">_nbPass</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp">    <span class="p">));</span></span>

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<td class="diff-line-num new_line" data-linenumber="276" style="width: 35px; color: rgba(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="LC276" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasMinimizerFrequencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_freq_order</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC279" 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;">storage</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;">Storage</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="n" style="color: #333;">os</span> <span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">,</span> <span class="s" style="color: #d14;">"minimRepart"</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="280" style="width: 35px; color: rgba(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="LC280" class="line" lang="cpp">    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span>                <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">));</span></span>

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<td class="diff-line-num new_line old" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp">    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_mm</span><span class="p">,</span>                    <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_mm</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp">    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nb_minims</span><span class="p">,</span>             <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nb_minims</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nbPass</span><span class="p">,</span>                <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">_nbPass</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp">    <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="n" style="color: #333;">_repart_table</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span>    <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Value</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_nb_minims</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(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="304" style="width: 35px; color: rgba(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">@@ -304,9 +304,8 @@ void Repartitor::save (tools::storage::impl::Group& group)</td>

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<pre style="margin: 0;"> <span id="LC304" 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="LC305" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Repartitor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printInfo</span> <span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nbMinimizers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">_mm</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp">    <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Repartitor : nbMinimizers=%ld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nbMinimizers</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nbMinimizers</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"   table[%ld] = %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">ii</span><span class="p">,</span><span class="n" style="color: #333;">_repart_table</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span> <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="310" 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="LC307" class="line" lang="cpp">    <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Repartitor : nbMinimizers=%ld</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_minims</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="310" 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="308" 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="LC308" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_nb_minims</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"   table[%ld] = %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">ii</span><span class="p">,</span><span class="n" style="color: #333;">_repart_table</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>

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<br>

</li>

<li id="8c129eb4ed08a953123df6cf51c678096ab15153">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#8c129eb4ed08a953123df6cf51c678096ab15153"><strong>gatb-core/src/gatb/kmer/impl/PartiInfo.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(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="24" style="width: 35px; color: rgba(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">@@ -24,6 +24,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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/kmer/impl/Model.hpp></span></span>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(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="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <gatb/tools/storage/impl/Storage.hpp></span></span>

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<td class="diff-line-num new old_line" data-linenumber="27" 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="27" 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="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <mutex></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC29" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/********************************************************************************/</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,16 +43,43 @@ namespace impl      {</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">xmer</span><span class="o" style="font-weight: 600;">></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PartiInfo</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="46" 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="LC46" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">mmer_bin_record</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="47" 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="LC47" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_superks</span><span class="p">,</span> <span class="n" style="color: #333;">nb_kmers</span><span class="p">,</span> <span class="n" style="color: #333;">nb_kxmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="48" 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="LC48" class="line" lang="cpp">        <span class="n" style="color: #333;">mmer_bin_record</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mmer_bin_record</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="49" 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="LC49" class="line" lang="cpp">            <span class="n" style="color: #333;">nb_superks</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">nb_superks</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="50" 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="LC50" class="line" lang="cpp">            <span class="n" style="color: #333;">nb_kmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">nb_kmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="51" 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="LC51" class="line" lang="cpp">            <span class="n" style="color: #333;">nb_kxmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">nb_kxmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="52" 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="LC52" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="53" 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="LC53" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" 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="LC55" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="56" 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="LC56" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">parti_record</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="57" 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="LC57" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_kmers</span><span class="p">,</span> <span class="n" style="color: #333;">nb_kxmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="58" 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="LC58" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nbk_per_radix</span><span class="p">[</span><span class="n" style="color: #333;">xmer</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">256</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="59" 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="LC59" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" 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="LC60" class="line" lang="cpp">        <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;">getNbKmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">radix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xx</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">        <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nbk_per_radix</span><span class="p">[</span><span class="n" style="color: #333;">xx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">256</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">radix</span><span class="p">];</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="62" 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">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">        <span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">            <span class="n" style="color: #333;">nb_kmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">nb_kmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="65" 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="LC65" class="line" lang="cpp">            <span class="n" style="color: #333;">nb_kxmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">nb_kxmers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="66" 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">

66

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<pre style="margin: 0;">+<span id="LC66" 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;">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;">xmer</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">256</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="67" 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="LC67" class="line" lang="cpp">                <span class="n" style="color: #333;">nbk_per_radix</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;">other</span><span class="p">.</span><span class="n" style="color: #333;">nbk_per_radix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="68" 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">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="69" 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">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="70" 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="LC70" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="45" 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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="nl">public:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC75" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">incKmer</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">nb_kmers_per_parti</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">parti_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kmers</span></span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>

</pre>

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50

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(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="LC79" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(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="LC80" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">incKxmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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53

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" 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">

54

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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">nb_kxmers_per_parti</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//now used to store number of kxmers per parti</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" 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="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">parti_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kxmers</span></span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//now used to store number of kxmers per parti</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(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="LC84" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(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="LC85" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//superksize in number of kmer inside this superk</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,73 +88,64 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">           <span class="n" style="color: #333;">_nb_superk_total</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(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="LC90" class="line" lang="cpp">           <span class="n" style="color: #333;">_nb_kmer_total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">superksize</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">superk_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">kmer_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">superksize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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="91" 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">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_superks</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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="92" 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="LC92" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kmers</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">superksize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(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="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//kxmer count (regardless of x size), used for ram</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">incKxmer_per_minimBin</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numbin</span><span class="p">,</span> <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(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="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">kxmer_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">        <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kxmers</span></span><span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(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="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(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="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//numaprt, radix, size of kx mer</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(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="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">incKmer_and_rad</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">radix</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="p">,</span>  <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//appele ds vrai loop</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kxmers_per_parti</span><span class="p">[</span><span class="n" style="color: #333;">numpart</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span>            <span class="c1" style="color: #998; font-style: italic;">// now used to store number of kxmers per parti</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kmers_per_parti</span> <span class="p">[</span><span class="n" style="color: #333;">numpart</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">));</span>  <span class="c1" style="color: #998; font-style: italic;">// number of  'real' kmers</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" 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="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">][</span><span class="n" style="color: #333;">radix</span><span class="p">][</span><span class="n" style="color: #333;">numpart</span><span class="p">]</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// contains number of kx mer per part per radix per x</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">        <span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_parti_records</span><span class="p">[</span><span class="n" style="color: #333;">numpart</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">nb_kxmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span>            <span class="c1" style="color: #998; font-style: italic;">// now used to store number of kxmers per parti</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">nb_kmers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">));</span>  <span class="c1" style="color: #998; font-style: italic;">// number of  'real' kmers</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">        <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">getNbKmer</span><span class="p">(</span><span class="n" style="color: #333;">radix</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">)</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// contains number of kx mer per part per radix per x</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" 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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="k" style="font-weight: 600;">operator</span><span class="o" style="font-weight: 600;">+=</span>  <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" 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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//add other parti info , synced</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" 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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" 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;">np</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;">np</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_nbpart</span><span class="p">;</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" 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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" 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;">size_t</span> <span class="n" style="color: #333;">xx</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;">xx</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xmer</span><span class="p">;</span> <span class="n" style="color: #333;">xx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" 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;">rad</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;">rad</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">rad</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp">                <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" 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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp">                    <span class="n" style="color: #333;">__sync_fetch_and_add</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xx</span><span class="p">][</span><span class="n" style="color: #333;">rad</span><span class="p">][</span><span class="n" style="color: #333;">np</span><span class="p">]),</span>   <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbKmer</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">,</span><span class="n" style="color: #333;">rad</span><span class="p">,</span><span class="n" style="color: #333;">xx</span><span class="p">)</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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

95

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"></span>

</pre>

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

96

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp">            <span class="n" style="color: #333;">__sync_fetch_and_add</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kmers_per_parti</span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbKmer</span>      <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">));</span></span>

</pre>

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

97

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp">            <span class="n" style="color: #333;">__sync_fetch_and_add</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kxmers_per_parti</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbSuperKmer</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">));</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Adds count to *this from other */</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PartiInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" 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;">np</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;">np</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">;</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">            <span class="n" style="color: #333;">_parti_records</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_parti_records</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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

114

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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

115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>

</pre>

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

100

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_num_mm_bins</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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

101

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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

102

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp">            <span class="n" style="color: #333;">__sync_fetch_and_add</span> <span class="p">(</span><span class="n" style="color: #333;">_superk_per_mmer_bin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbSuperKmer_per_minim</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">));</span></span>

</pre>

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

103

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp">            <span class="n" style="color: #333;">__sync_fetch_and_add</span> <span class="p">(</span><span class="n" style="color: #333;">_kmer_per_mmer_bin</span>   <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbKmer_per_minim</span>      <span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">));</span></span>

</pre>

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

104

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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp">            <span class="n" style="color: #333;">__sync_fetch_and_add</span> <span class="p">(</span><span class="n" style="color: #333;">_kxmer_per_mmer_bin</span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">getNbKxmer_per_minim</span>     <span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">));</span></span>

</pre>

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

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

116

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<pre style="margin: 0;">+<span id="LC116" 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;">ii</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;">ii</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_num_mm_bins</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="cpp">            <span class="n" style="color: #333;">_mmer_bin_records</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_mmer_bin_records</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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

106

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp">          <span class="n" style="color: #333;">__sync_fetch_and_add</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nb_superk_total</span> <span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_nb_superk_total</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

108

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp">          <span class="n" style="color: #333;">__sync_fetch_and_add</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_nb_kmer_total</span> <span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_nb_kmer_total</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" 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">

109

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp">          </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" 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">

110

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="120" 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="LC120" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_superk_total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_nb_superk_total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" 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="LC121" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kmer_total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">_nb_kmer_total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" 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">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

123

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<pre style="margin: 0;"> <span id="LC123" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(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="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="126" 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="LC126" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Adds count to *this from other while preventing concurrent access to *this */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="127" 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="LC127" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">add_sync</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PartiInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Locking is way faster than doing individuals "lock add"s for all the fields</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" 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;">guard</span><span class="p">{</span><span class="n" style="color: #333;">_mut</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="130" 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="LC130" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="131" 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="LC131" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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

<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>

</pre>

</td>

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

114

</td>

<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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

<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

</td>

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

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

115

</td>

<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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

<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">getNbKmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

</td>

<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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

<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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

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

117

</td>

<td class="diff-line-num new_line old" data-linenumber="136" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">nb_kmers_per_parti</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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

<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">parti_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kmers</span></span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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

<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

</td>

<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

</td>

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

<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

</td>

<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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

<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Get nbk in bin radix of parti numpart */</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

</td>

<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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

<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">getNbKmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">radix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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

<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="123" 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">

123

</td>

<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">nbk_per_radix_per_part</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">xx</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">radix</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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

<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">parti_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">getNbKmer</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">radix</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xx</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

</td>

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

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

124

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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

<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

</td>

<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

144

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

<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

</td>

<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

145

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

<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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

<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span>   <span class="n" style="color: #333;">getNbSuperKmer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numpart</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="c1" style="color: #998; font-style: italic;">//now used for number of kxmers (indistinctive of xsize)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="diff-line-num new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

147

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

<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="129" 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">

129

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<td class="diff-line-num new_line old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">nb_kxmers_per_parti</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" 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="148" 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="LC148" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">parti_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numpart</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kxmers</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

131

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span>   <span class="n" style="color: #333;">getNbSuperKmerTotal</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(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">@@ -141,37 +160,26 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(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="LC160" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(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="LC161" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span>   <span class="n" style="color: #333;">getNbSuperKmer_per_minim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numbin</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" 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="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">superk_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="163" 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="LC163" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_superks</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(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="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(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="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(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="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span>   <span class="n" style="color: #333;">getNbKmer_per_minim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numbin</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(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="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="150" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">kmer_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="169" 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="LC169" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kmers</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

171

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

<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<td class="diff-line-num new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

172

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

<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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

<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span>  <span class="n" style="color: #333;">u_int64_t</span>   <span class="n" style="color: #333;">getNbKxmer_per_minim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numbin</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num 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">

155

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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

<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

156

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<td class="diff-line-num new_line old" data-linenumber="175" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">kxmer_per_mmer_bin</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="175" 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">

175

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

<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_<span class="idiff left">mmer_bin_records</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">numbin</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">nb_kxmers</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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

<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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

<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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

<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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

<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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

<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kmers_per_parti</span><span class="p">,</span>  <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_nbpart</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;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kxmers_per_parti</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_nbpart</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;">u_int64_t</span><span class="p">));</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_superk_per_mmer_bin</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_num_mm_bins</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;">u_int64_t</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_kmer_per_mmer_bin</span><span class="p">,</span>   <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_num_mm_bins</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;">u_int64_t</span><span class="p">));</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_kxmer_per_mmer_bin</span><span class="p">,</span>  <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_num_mm_bins</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;">u_int64_t</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

168

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" 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;">size_t</span> <span class="n" style="color: #333;">xx</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;">xx</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xmer</span><span class="p">;</span> <span class="n" style="color: #333;">xx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="169" 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">

169

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" 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">

170

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" 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;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="171" 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">

171

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" 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">

172

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp">                <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xx</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_nbpart</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;">u_int64_t</span><span class="p">));</span></span>

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<td class="diff-line-num old old_line" data-linenumber="173" 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">

173

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" 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">

174

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" 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="181" 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="LC181" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_parti_records</span><span class="p">,</span>    <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_nbpart</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;">parti_record</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" 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="182" 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">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">        <span class="n" style="color: #333;">memset</span> <span class="p">(</span><span class="n" style="color: #333;">_mmer_bin_records</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_num_mm_bins</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;">mmer_bin_record</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<td class="diff-line-num new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

183

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(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="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(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="217" style="width: 35px; color: rgba(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">@@ -209,12 +217,8 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="209" style="width: 35px; color: rgba(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="217" style="width: 35px; color: rgba(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="LC217" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(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="LC218" 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;">np</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;">np</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">;</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" 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="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Kmer</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">31</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span>           <span class="n" style="color: #333;">Typem</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//should be kmer size</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="213" 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="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp">            <span class="n" style="color: #333;">Typem</span> <span class="n" style="color: #333;">cur</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp">            <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">setVal</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(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="LC220" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbSuperKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="217" 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="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp">                          <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bin[%5i<span class="idiff left"> (%s) ]= %lli    %lli</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">cur</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">toString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_mm</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbSuperKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">),</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">)</span>    <span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="218" 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="221" 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="LC221" class="line" lang="cpp">                          <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bin[%5i<span class="idiff left">]= %lli    %lli</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">np</span></span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbSuperKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">),</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">)</span>    <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">            <span class="n" style="color: #333;">sumk</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC224" class="line" lang="cpp">            <span class="n" style="color: #333;">sumsuperk</span> <span class="o" style="font-weight: 600;">+=</span>  <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNbSuperKmer_per_minim</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="225" style="width: 35px; color: rgba(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="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -225,49 +229,27 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Constructor. */</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbpart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_mm</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">minimsize</span></span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbpart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="233" style="width: 35px; color: rgba(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="LC233" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="234" style="width: 35px; color: rgba(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="LC234" class="line" lang="cpp">          <span class="n" style="color: #333;">_nb_superk_total</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">          <span class="n" style="color: #333;">_nb_kmer_total</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="232" 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="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kmers_per_parti</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="233" 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="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kxmers_per_parti</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp">        <span class="n" style="color: #333;">_num_mm_bins</span> <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">1</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;">_mm</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp">        <span class="n" style="color: #333;">_superk_per_mmer_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp">        <span class="n" style="color: #333;">_kmer_per_mmer_bin</span>   <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp">        <span class="n" style="color: #333;">_kxmer_per_mmer_bin</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC239" 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;">size_t</span> <span class="n" style="color: #333;">xx</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;">xx</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xmer</span><span class="p">;</span> <span class="n" style="color: #333;">xx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp">            <span class="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;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp">                <span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xx</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">        <span class="n" style="color: #333;">_parti_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">parti_record</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">        <span class="n" style="color: #333;">_num_mm_bins</span> <span class="o" style="font-weight: 600;">=</span>   <span class="mi" style="color: #099;">1</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;">minimsize</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">        <span class="n" style="color: #333;">_mmer_bin_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">mmer_bin_record</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">mmer_bin_record</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Constructor (copy). Needed for fillparti class. */</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cr</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//the copy contr realloc its own  arrays, zero init</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">        <span class="n" style="color: #333;">_num_mm_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cr</span><span class="p">.</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">        <span class="n" style="color: #333;">_nbpart</span>      <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cr</span><span class="p">.</span><span class="n" style="color: #333;">_nbpart</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp">        <span class="n" style="color: #333;">_mm</span>          <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cr</span><span class="p">.</span><span class="n" style="color: #333;">_mm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">          <span class="n" style="color: #333;">_nb_superk_total</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cr</span><span class="p">.</span><span class="n" style="color: #333;">_nb_superk_total</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">          <span class="n" style="color: #333;">_nb_kmer_total</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cr</span><span class="p">.</span><span class="n" style="color: #333;">_nb_kmer_total</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">          </span>

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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kmers_per_parti</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span>      <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp">        <span class="n" style="color: #333;">_nb_kxmers_per_parti</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span>      <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

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<td class="diff-line-num old old_line" data-linenumber="260" 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">

260

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp">        <span class="n" style="color: #333;">_superk_per_mmer_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="261" 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">

261

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp">        <span class="n" style="color: #333;">_kmer_per_mmer_bin</span>   <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="262" 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">

262

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp">        <span class="n" style="color: #333;">_kxmer_per_mmer_bin</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

263

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<td class="diff-line-num new_line old" data-linenumber="251" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="264" 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">

264

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC264" 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;">size_t</span> <span class="n" style="color: #333;">xx</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;">xx</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xmer</span><span class="p">;</span> <span class="n" style="color: #333;">xx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="265" 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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="266" 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">

266

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC266" 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;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="267" 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">

267

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="268" 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">

268

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp">                <span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xx</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span>  <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span><span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="269" 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">

269

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="270" 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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp">        <span class="n" style="color: #333;">_parti_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_nbpart</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">parti_record</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">        <span class="n" style="color: #333;">_mmer_bin_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">mmer_bin_record</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span> <span class="p">(</span><span class="n" style="color: #333;">_num_mm_bins</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">mmer_bin_record</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

271

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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

253

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

<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

272

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

254

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//    printf("PartiInfo copy constr %p  _nb_kmers_per_parti %p \n",this,_nb_kmers_per_parti);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

273

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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

255

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" style="width: 35px; color: rgba(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">@@ -276,32 +258,18 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC258" 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="LC259" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">PartiInfo</span><span class="p">()</span></span>

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

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kmers_per_parti</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_nb_kxmers_per_parti</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_superk_per_mmer_bin</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_kmer_per_mmer_bin</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_kxmer_per_mmer_bin</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC285" 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;">size_t</span> <span class="n" style="color: #333;">xx</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;">xx</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">xmer</span><span class="p">;</span> <span class="n" style="color: #333;">xx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>  <span class="p">{</span>  <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;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">256</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>  <span class="p">{</span>  <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xx</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span>  <span class="p">}</span>  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//    printf("print info destroyed %p  _nb_kmers_per_parti %p \n",this,_nb_kmers_per_parti);</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_parti_records</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="262" 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="LC262" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_mmer_bin_records</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp">    <span class="p">}</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_nb_kmers_per_parti</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="293" 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">

293

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_nb_kxmers_per_parti</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//now used to store number of kxmers per parti</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="294" 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">

294

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_superk_per_mmer_bin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="295" 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">

295

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp">  <span class="n" style="color: #333;">u_int64_t</span>  <span class="n" style="color: #333;">_nb_superk_total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="296" 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">

296

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp">  <span class="n" style="color: #333;">u_int64_t</span>  <span class="n" style="color: #333;">_nb_kmer_total</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="297" 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">

297

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_kmer_per_mmer_bin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="298" 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">

298

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_kxmer_per_mmer_bin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="299" 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">

299

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<td class="diff-line-num new_line old" data-linenumber="266" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="300" 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">

300

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<td class="diff-line-num new_line old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_nbk_per_radix_per_part</span><span class="p">[</span><span class="n" style="color: #333;">xmer</span><span class="p">][</span><span class="mi" style="color: #099;">256</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//number of kxmer per parti per rad</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="266" 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="LC266" 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;">_mut</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span> <span class="c1" style="color: #998; font-style: italic;">// Locking for merging with main PartiInfo</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="301" 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="267" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(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="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">_num_mm_bins</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" 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="269" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="303" 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="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="304" 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="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_mm</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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

<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">  <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">_nb_superk_total</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="270" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">  <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">_nb_kmer_total</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="271" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">    <span class="n" style="color: #333;">parti_record</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">_parti_records</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="272" 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="LC272" class="line" lang="cpp">    <span class="n" style="color: #333;">mmer_bin_record</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">_mmer_bin_records</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC275" 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">@@ -331,13 +299,13 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Constructor</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] nbpart : hash value will be in range [0..nbpart-1]</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     * \param[in] minimsize : size of the minimizers. */</span></span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp">    <span class="n" style="color: #333;">Repartitor</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbpart</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimsize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbPass</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">),</span> <span class="n" style="color: #333;">_<span class="idiff left">mm</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">minimsize</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_nb_minims</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">_mm</span></span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">)),</span> <span class="n" style="color: #333;">_nbPass</span><span class="p">(</span><span class="n" style="color: #333;">nbPass</span><span class="p">),</span> <span class="n" style="color: #333;">_freq_order</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="LC302" class="line" lang="cpp">    <span class="n" style="color: #333;">Repartitor</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbpart</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimsize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbPass</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="n" style="color: #333;">nbpart</span><span class="p">),</span> <span class="n" style="color: #333;">_<span class="idiff left">nb_minims</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">minimsize</span></span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">)),</span> <span class="n" style="color: #333;">_nbPass</span><span class="p">(</span><span class="n" style="color: #333;">nbPass</span><span class="p">),</span> <span class="n" style="color: #333;">_freq_order</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="LC303" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nbpart</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>  <span class="p">{</span> <span class="n" style="color: #333;">system</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Repartitor: nbpart (%d) should be > 0"</span><span class="p">,</span> <span class="n" style="color: #333;">nbpart</span><span class="p">);</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Constructor */</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp">    <span class="n" style="color: #333;">Repartitor</span> <span class="p">(</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">storage</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;">Group</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_<span class="idiff left">mm</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>nb_minims</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_nbPass</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_freq_order</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="p">{</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load</span> <span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">);</span>  <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="341" 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="308" 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="LC308" class="line" lang="cpp">    <span class="n" style="color: #333;">Repartitor</span> <span class="p">(</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">storage</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;">Group</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">group</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_nbpart</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_nb_minims</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_nbPass</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">_freq_order</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="p">{</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load</span> <span class="p">(</span><span class="n" style="color: #333;">group</span><span class="p">);</span>  <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="341" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Destructor */</span></span>

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<td class="diff-line-num old_line" data-linenumber="343" style="width: 35px; color: rgba(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="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="n" style="color: #333;">Repartitor</span> <span class="p">()</span>  <span class="p">{</span>  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_freq_order</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">_freq_order</span><span class="p">;</span> <span class="p">}</span> <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="379" style="width: 35px; color: rgba(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">@@ -411,7 +379,6 @@ private:</td>

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

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<td class="diff-line-num new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int16_t</span>          <span class="n" style="color: #333;">_nbpart</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="414" 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="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int16_t</span>          <span class="n" style="color: #333;">_mm</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="415" style="width: 35px; color: rgba(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="382" style="width: 35px; color: rgba(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="LC382" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span>          <span class="n" style="color: #333;">_nb_minims</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="416" style="width: 35px; color: rgba(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="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int16_t</span>          <span class="n" style="color: #333;">_nbPass</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp">    <span class="n" style="color: #333;">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;">Value</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_repart_table</span> <span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="d6e7c785a22fb981430b2e12eed55480273715bf">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#d6e7c785a22fb981430b2e12eed55480273715bf"><strong>gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -182,7 +182,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">superKmerLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

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<td class="diff-line-num new_line" data-linenumber="183" style="width: 35px; color: rgba(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="LC183" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(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="184" style="width: 35px; color: rgba(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="LC184" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** We increase superkmer counter the current minimizer. */</span></span>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp">            <span class="n" style="color: #333;">_<span class="idiff left right">local_</span>pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incSuperKmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">,</span> <span class="n" style="color: #333;">superKmerLen</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">            <span class="n" style="color: #333;">_pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incSuperKmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">,</span> <span class="n" style="color: #333;">superKmerLen</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** We loop over the kmer of the superkmer (except the first one).</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">             *  We update the pInfo each time we find a kxmer in the superkmer. */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(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="193" style="width: 35px; color: rgba(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">@@ -193,7 +193,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">which</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">prev_which</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">kx_size</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">_kx</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// kxmer_size = 1 //cost should diminish with larger kxmer</span></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp">                <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp">                    <span class="cm" style="color: #998; font-style: italic;">/** We increase the number of kxmer found for the current minimizer. */</span></span>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cpp">                    <span class="n" style="color: #333;">_<span class="idiff left right">local_</span>pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incKxmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp">                    <span class="n" style="color: #333;">_pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incKxmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">                    <span class="n" style="color: #333;">kx_size</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="LC198" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">else</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(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="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">            <span class="p">}</span></span>

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

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(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="LC207" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** We add the pending kxmer to the bin. */</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp">            <span class="n" style="color: #333;">_<span class="idiff left right">local_</span>pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incKxmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">            <span class="n" style="color: #333;">_pInfo</span><span class="p">.</span><span class="n" style="color: #333;">incKxmer_per_minimBin</span> <span class="p">(</span><span class="n" style="color: #333;">superKmer</span><span class="p">.</span><span class="n" style="color: #333;">minimizer</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp">        </span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// see if we need to stop</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp">            <span class="n" style="color: #333;">_nbSuperKmersSeenSoFar</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -221,8 +221,6 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">    <span class="n" style="color: #333;">SampleRepart</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">        <span class="n" style="color: #333;">Model</span><span class="o" style="font-weight: 600;">&</span>            <span class="n" style="color: #333;">model</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;">Configuration</span><span class="o" style="font-weight: 600;">&</span>    <span class="n" style="color: #333;">config</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span>            <span class="n" style="color: #333;">nbPasses</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span>            <span class="n" style="color: #333;">currentPass</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span>            <span class="n" style="color: #333;">nbPartitions</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp">        <span class="n" style="color: #333;">IteratorListener</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span>            <span class="n" style="color: #333;">cancelIterator</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="230" style="width: 35px; color: rgba(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="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp">        <span class="n" style="color: #333;">BankStats</span><span class="o" style="font-weight: 600;">&</span>        <span class="n" style="color: #333;">bankStats</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">        <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">>&</span>     <span class="n" style="color: #333;">pInfo</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">    <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">:</span>   <span class="n" style="color: #333;">Sequence2SuperKmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">nbPasses</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">currentPass</span></span><span class="p">,</span> <span class="n" style="color: #333;">nbPartitions</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">bankStats</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp">        <span class="p">,</span><span class="n" style="color: #333;">_kx</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="n" style="color: #333;">_<span class="idiff left">extern_pInfo</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pInfo</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_local_pInfo</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_nb_partitions</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">model</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getMmersModel</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">getKmerSize</span></span><span class="p"><span class="idiff right">()</span>),</span></span>

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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">:</span>   <span class="n" style="color: #333;">Sequence2SuperKmer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span> <span class="n" style="color: #333;">nbPartitions</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">bankStats</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">        <span class="p">,</span><span class="n" style="color: #333;">_kx</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">),</span> <span class="n" style="color: #333;">_<span class="idiff left">pInfo</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">pInfo</span></span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">        <span class="n" style="color: #333;">_cancelIterator</span><span class="p">(</span><span class="n" style="color: #333;">cancelIterator</span><span class="p">),</span> <span class="n" style="color: #333;">_nbSeqsToSee</span><span class="p">(</span><span class="n" style="color: #333;">nbSeqsToSee</span><span class="p">),</span> <span class="n" style="color: #333;">_nbSuperKmersSeenSoFar</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="234" style="width: 35px; color: rgba(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="LC234" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(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="LC236" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Destructor. */</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">SampleRepart</span> <span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//add to global parti_info</span></span>

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<td class="diff-line-num old old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp">        <span class="n" style="color: #333;">_extern_pInfo</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_local_pInfo</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"><span class="nl">private:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span>        <span class="n" style="color: #333;">_kx</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">_<span class="idiff left right">extern_</span>pInfo</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"><span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">PartiInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff">  </span><span class="n" style="color: #333;"><span class="idiff">_local_pInfo</span></span><span class="p"><span class="idiff right">;</span></span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">    <span class="n" style="color: #333;">PartiInfo</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">_pInfo</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">*</span>         <span class="n" style="color: #333;">_cancelIterator</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span>        <span class="n" style="color: #333;">_nbSeqsToSee</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span>        <span class="n" style="color: #333;">_nbSuperKmersSeenSoFar</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="323" style="width: 35px; color: rgba(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">@@ -332,6 +323,9 @@ void RepartitorAlgorithm<span>::computeFrequencies (Repartitor& repartitor)</td>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">nbseq_sample</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;">min</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;">estimateSeqNb</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.05</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="mi" style="color: #099;">50000000ULL</span><span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// TODO would be better to just stop estimating minimizer frequency when it becomes stable. not after a fixed number of reads</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nbseq_sample</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="LC327" class="line" lang="cpp">        <span class="n" style="color: #333;">nbseq_sample</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="LC328" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp">    <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">rg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">u_int64_t</span><span class="p">)</span><span class="mi" style="color: #099;">1</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;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_minim_size</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//cout << "\nAllocating " << ((rg*sizeof(uint32_t))/1024) << " KB for " << _minim_size <<"-mers frequency counting (" << rg << " elements total)" << endl;</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp">    <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;">m_mer_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">[</span><span class="n" style="color: #333;">rg</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -426,52 +420,14 @@ void RepartitorAlgorithm<span>::computeRepartition (Repartitor& repartitor)</td>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp">        <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</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;">_bank</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;">LOCAL</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*></span> <span class="n" style="color: #333;">itBanks</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;">getComposition</span><span class="p">();</span> </span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC429" 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="LC430" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">        bool dummyBoolean = false;</span></span>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">        SampleRepart<span> sampleRepart (</span></span>

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      model,</span></span>

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      _config,</span></span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      1, // we don't care about the actual number of passes, we just use 1</span></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      0, // we don't care about the actual number of passes, the current one is 0</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      _config._nb_partitions,</span></span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      NULL,</span></span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      &dummyBoolean, // will be set to true when iteration needs to be stopped</span></span>

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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      nbseq_sample, // how many sequences we need to see</span></span>

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      bstatsDummy,</span></span>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      sample_info</span></span>

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<pre style="margin: 0;">-<span id="LC442" 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="LC443" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//SerialDispatcher serialDispatcher;</span></span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//BankStats bstatsDummy;</span></span>

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

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<pre style="margin: 0;"> <span id="LC423" 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;">size_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;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_banks</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="LC448" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//cout << i << endl;</span></span>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//u_int64_t nbseq_sample_ = min(nbseq_sample, u_int64_t (500000));</span></span>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//TruncateIterator<Sequence>* it = new TruncateIterator<Sequence> (*(itBanks[i]), nbseq_sample_);</span></span>

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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//LOCAL(it);</span></span>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp">              <span class="c1" style="color: #998; font-style: italic;">//serialDispatcher.iterate (it, sampleRepart);</span></span>

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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//Iterator<Sequence>* bankit = itBanks[i];</span></span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//LOCAL(bankit);</span></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp">            <span class="n" style="color: #333;">CancellableIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">cancellable_it</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CancellableIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp">            <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">cancellable_it</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//cout << nbseq_sample << endl;</span></span>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp">                  <span class="cm" style="color: #998; font-style: italic;">/** We create a sequence iterator and give it a progress message */</span></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">//Iterator<Sequence>* it_all_reads = createIterator<Sequence> (</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//                cancellable_it,</span></span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//                _bank->getNbItems(),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//                Stringify::format (progressFormat0, bankShortName.c_str()).c_str()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//                );</span></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//LOCAL (it_all_reads);</span></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

469

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp">                  <span class="cm" style="color: #998; font-style: italic;">/** We compute a distribution of Superkmers from a part of the bank. */</span></span>

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<td class="diff-line-num old_line" data-linenumber="470" style="width: 35px; color: rgba(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="LC428" class="line" lang="cpp">                  <span class="n" style="color: #333;">serialDispatcher</span><span class="p">.</span><span class="n" style="color: #333;">iterate</span> <span class="p">(</span><span class="n" style="color: #333;">cancellable_it</span><span class="p">,</span> <span class="n" style="color: #333;">SampleRepart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp">                          <span class="n" style="color: #333;">model</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp">                          <span class="n" style="color: #333;">_config</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="cpp">                          <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// we don't care about the actual number of passes, we just use 1</span></span>

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<td class="diff-line-num new_line old" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp">                          <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// we don't care about the actual number of passes, the current one is 0</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp">                          <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp">                          <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="433" style="width: 35px; color: rgba(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="LC433" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cancellable_it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_cancel</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// will be set to true when iteration needs to be stopped</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="493" style="width: 35px; color: rgba(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="449" style="width: 35px; color: rgba(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">@@ -493,11 +449,9 @@ void RepartitorAlgorithm<span>::computeRepartition (Repartitor& repartitor)</td>

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<td class="diff-line-num new_line" data-linenumber="449" style="width: 35px; color: rgba(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="LC449" class="line" lang="cpp">        <span class="n" style="color: #333;">CancellableIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">cancellable_it</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CancellableIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

450

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp">        <span class="n" style="color: #333;">LOCAL</span><span class="p">(</span><span class="n" style="color: #333;">cancellable_it</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="diff-line-num new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

451

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="496" 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="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(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="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// how many seqs we need to see</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(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="LC453" class="line" lang="cpp">          <span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">nbseq_sample</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;">max</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;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_estimateSeqNb</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.05</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="mi" style="color: #099;">1000000ULL</span><span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(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="454" style="width: 35px; color: rgba(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="LC454" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="500" 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="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//cout << nbseq_sample << endl;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" style="width: 35px; color: rgba(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="LC455" class="line" lang="cpp">          <span class="cm" style="color: #998; font-style: italic;">/** We create a sequence iterator and give it a progress message */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

502

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<td class="diff-line-num new_line" data-linenumber="456" style="width: 35px; color: rgba(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="LC456" class="line" lang="cpp">          <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">it_all_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createIterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>

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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(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="457" style="width: 35px; color: rgba(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="LC457" class="line" lang="cpp">                          <span class="n" style="color: #333;">cancellable_it</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="506" style="width: 35px; color: rgba(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="460" style="width: 35px; color: rgba(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">@@ -506,7 +460,6 @@ void RepartitorAlgorithm<span>::computeRepartition (Repartitor& repartitor)</td>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(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="LC460" class="line" lang="cpp">                          <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="507" style="width: 35px; color: rgba(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="461" style="width: 35px; color: rgba(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="LC461" class="line" lang="cpp">          <span class="n" style="color: #333;">LOCAL</span> <span class="p">(</span><span class="n" style="color: #333;">it_all_reads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="508" style="width: 35px; color: rgba(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="462" style="width: 35px; color: rgba(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="LC462" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="509" 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">

509

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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<td class="diff-line-num new_line" data-linenumber="463" style="width: 35px; color: rgba(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="LC463" class="line" lang="cpp">          <span class="n" style="color: #333;">BankStats</span> <span class="n" style="color: #333;">bstatsDummy</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="464" style="width: 35px; color: rgba(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="LC464" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="512" style="width: 35px; color: rgba(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="465" style="width: 35px; color: rgba(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="LC465" class="line" lang="cpp">          <span class="cm" style="color: #998; font-style: italic;">/** We compute a distribution of Superkmers from a part of the bank. */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="514" style="width: 35px; color: rgba(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="467" style="width: 35px; color: rgba(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">@@ -514,8 +467,6 @@ void RepartitorAlgorithm<span>::computeRepartition (Repartitor& repartitor)</td>

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<td class="diff-line-num old_line" data-linenumber="514" style="width: 35px; color: rgba(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="467" style="width: 35px; color: rgba(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="LC467" class="line" lang="cpp">          <span class="n" style="color: #333;">serialDispatcher</span><span class="p">.</span><span class="n" style="color: #333;">iterate</span> <span class="p">(</span><span class="n" style="color: #333;">it_all_reads</span><span class="p">,</span> <span class="n" style="color: #333;">SampleRepart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="515" style="width: 35px; color: rgba(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="468" style="width: 35px; color: rgba(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="LC468" class="line" lang="cpp">                  <span class="n" style="color: #333;">model</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(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="469" style="width: 35px; color: rgba(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="LC469" class="line" lang="cpp">                  <span class="n" style="color: #333;">_config</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC517" class="line" lang="cpp">                  <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// we don't care about the actual number of passes, we just use 1</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp">                  <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// we don't care about the actual number of passes, the current one is 0</span></span>

</pre>

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519

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<td class="diff-line-num new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

470

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp">                  <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

520

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<td class="diff-line-num new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

471

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp">                  <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

521

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<td class="diff-line-num new_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

472

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp">                  <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cancellable_it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_cancel</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">// will be set to true when iteration needs to be stopped</span></span>

</pre>

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<br>

</li>

<li id="ed783240a52e80bd1c3a470d6646b3f6b3ab63e4">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#ed783240a52e80bd1c3a470d6646b3f6b3ab63e4"><strong>gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="867" style="width: 35px; color: rgba(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="867" style="width: 35px; color: rgba(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">@@ -867,12 +867,12 @@ public:</td>

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867

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867

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<pre style="margin: 0;"> <span id="LC867" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="868" style="width: 35px; color: rgba(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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868

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

869

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869

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/** Destructor. */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="870" 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">

870

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<td class="diff-line-num new_line old" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC870" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="870" 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">

870

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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp">  <span class="k" style="font-weight: 600;"><span class="idiff left">virtual</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

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871

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871

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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

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872

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<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//printf("destruc fillparti _superkmerFiles %p \n",_superkmerFiles);</span></span>

</pre>

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873

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873

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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp">          </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

874

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874

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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//add to global parti_info</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="875" 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">

875

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<td class="diff-line-num new_line old" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC875" class="line" lang="cpp">          <span class="n" style="color: #333;">_extern_pInfo</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 right">_local_pInfo</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="876" 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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875

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp">          <span class="n" style="color: #333;">_extern_pInfo</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_sync</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_local_pInfo</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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876

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="877" style="width: 35px; color: rgba(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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877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="878" style="width: 35px; color: rgba(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="878" style="width: 35px; color: rgba(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="LC878" class="line" lang="cpp"><span class="nl">private:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1007" style="width: 35px; color: rgba(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="1007" style="width: 35px; color: rgba(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">@@ -1007,12 +1007,12 @@ public:</td>

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1007

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<td class="diff-line-num new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1007

</td>

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

<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1008

</td>

<td class="diff-line-num new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1008

</td>

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

<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1009

</td>

<td class="diff-line-num new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1009

</td>

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

<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Destructor. */</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1010" 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">

1010

</td>

<td class="diff-line-num new_line old" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1010" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1010" 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">

1010

</td>

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

<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">virtual</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1011

</td>

<td class="diff-line-num new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1011

</td>

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

<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

</td>

<td class="diff-line-num new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1012

</td>

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

<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">//printf("destruc fillparti _superkmerFiles %p \n",_superkmerFiles);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

</td>

<td class="diff-line-num new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

</td>

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

<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

</td>

<td class="diff-line-num new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

</td>

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

<pre style="margin: 0;"> <span id="LC1014" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//add to global parti_info</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1015" 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">

1015

</td>

<td class="diff-line-num new_line old" data-linenumber="1015" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1015" class="line" lang="cpp">        <span class="n" style="color: #333;">_extern_pInfo</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 right">_local_pInfo</span></span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1015" 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">

1015

</td>

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

<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp">        <span class="n" style="color: #333;">_extern_pInfo</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_sync</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_local_pInfo</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

</td>

<td class="diff-line-num new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

</td>

<td class="diff-line-num new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

</td>

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

<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

</td>

<td class="diff-line-num new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

</td>

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

<pre style="margin: 0;"> <span id="LC1018" class="line" lang="cpp"><span class="nl">private:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1143" style="width: 35px; color: rgba(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="1143" style="width: 35px; color: rgba(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">@@ -1143,12 +1143,12 @@ private:</td>

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<td class="diff-line-num old_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

</td>

<td class="diff-line-num new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

</td>

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

<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">         </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1144

</td>

<td class="diff-line-num new_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1144

</td>

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

<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp">         </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1145

</td>

<td class="diff-line-num new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1145

</td>

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

<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp">         <span class="cm" style="color: #998; font-style: italic;">/** Destructor. */</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1146" 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">

1146

</td>

<td class="diff-line-num new_line old" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1146" class="line" lang="cpp">         <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1146" 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">

1146

</td>

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

<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp">         <span class="k" style="font-weight: 600;"><span class="idiff left">virtual</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FillPartitions</span> <span class="p">()</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1147

</td>

<td class="diff-line-num new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1147

</td>

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

<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1148

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<td class="diff-line-num new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1148

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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">//printf("destruc fillparti _superkmerFiles %p \n",_superkmerFiles);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1149

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<td class="diff-line-num new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1149

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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp">                 </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1150

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<td class="diff-line-num new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1150

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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">//add to global parti_info</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1151" 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">

1151

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<td class="diff-line-num new_line old" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="cpp">                 <span class="n" style="color: #333;">_extern_pInfo</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 right">_local_pInfo</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1152" 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="1151" 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">

1151

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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="cpp">                 <span class="n" style="color: #333;">_extern_pInfo</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">add_sync</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_local_pInfo</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

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<td class="diff-line-num new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1153" style="width: 35px; color: rgba(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="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1153

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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1154

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<td class="diff-line-num new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1154

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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="cpp"> <span class="nl">private:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1183" style="width: 35px; color: rgba(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="1183" style="width: 35px; color: rgba(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">@@ -1183,6 +1183,7 @@ void SortingCountAlgorithm<span>::fillPartitions (size_t pass, Iterator<Sequence</td>

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1183

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<td class="diff-line-num new_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1183

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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1184

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<td class="diff-line-num new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1184

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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp">         <span class="n" style="color: #333;">DEBUG</span> <span class="p">((</span><span class="s" style="color: #d14;">"SortingCountAlgorithm<span>::fillPartitions  _kmerSize=%d _minim_size=%d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_minim_size</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1185

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<td class="diff-line-num new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1185

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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp">         </span>

</pre>

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

1186

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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="cpp">         <span class="n" style="color: #333;">_nbKmersPerPartitionPerBank</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1186

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<td class="diff-line-num new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1187

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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1188

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1188

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<td class="diff-line-num new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1189

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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We delete the previous partitions storage. */</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1226" style="width: 35px; color: rgba(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="1227" style="width: 35px; color: rgba(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">@@ -1226,72 +1227,79 @@ void SortingCountAlgorithm<span>::fillPartitions (size_t pass, Iterator<Sequence</td>

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1226

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<td class="diff-line-num new_line" data-linenumber="1227" style="width: 35px; color: rgba(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="LC1227" class="line" lang="cpp">         <span class="cm" style="color: #998; font-style: italic;">/** We have to reinit the progress instance since it may have been used by SampleRepart before. */</span></span>

</pre>

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1227

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<td class="diff-line-num new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1228

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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp">         <span class="n" style="color: #333;">_progress</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">init</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1228" style="width: 35px; color: rgba(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="1229" style="width: 35px; color: rgba(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="LC1229" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1229" 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">

1229

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="cpp">         <span class="cm" style="color: #998; font-style: italic;">/** We may have several input banks instead of a single one. */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1230" 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">

1230

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="cpp">         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*></span> <span class="n" style="color: #333;">itBanks</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComposition</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1231" 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">

1231

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1232" 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">

1232

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="cpp">         <span class="cm" style="color: #998; font-style: italic;">/** We first reset the vector holding the kmers number for each partition and for each bank.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1233" 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">

1233

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              * It can be seen as the following matrix:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1234" 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">

1234

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1234" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1235" 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">

1235

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *           part0  part1  part2 ... partJ</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1236" 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">

1236

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1236" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *   bank0    xxx    xxx    xxx       xxx</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1237" 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">

1237

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1237" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *   bank1    xxx    xxx    xxx       xxx</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1238" 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">

1238

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1238" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *    ...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1239" 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">

1239

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1239" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *   bankI    xxx    xxx    xxx       xxx</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1240" 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">

1240

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1240" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1241" 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">

1241

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1241" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              *   Here xxx is the number of items found for the bank I in the partition J</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1242" 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">

1242

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1242" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">              */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1243" 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">

1243

</td>

<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="cpp">         <span class="n" style="color: #333;">_nbKmersPerPartitionPerBank</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1244" 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">

1244

</td>

<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="cpp">         </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1245" 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">

1245

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1245" class="line" lang="cpp">         <span class="cm" style="color: #998; font-style: italic;">/** We launch the iteration of the sequences iterator with the created functors. */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1246" 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">

1246

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1246" 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;">size_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;">itBanks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1247" 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">

1247

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<pre style="margin: 0;">-<span id="LC1247" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1248" 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">

1248

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<td class="diff-line-num new_line old" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">groupSize</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1230" 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="LC1230" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1231" 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">

1231

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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We launch the iteration of the sequences iterator with the created</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1232" 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">

1232

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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      * functors. */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1233" 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">

1233

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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1249" 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="1234" 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">

1234

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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">groupSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1249

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<td class="diff-line-num new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="cpp">                 <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">deleteSynchro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1250" 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">

1250

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1250" class="line" lang="cpp">                 </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1251" 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">

1251

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1251" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We fill the partitions. Each thread will read synchronously and will call FillPartitions</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1252" 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">

1252

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1252" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      * in a synchronous way (in order to have global BanksStats correctly computed). */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1253" 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">

1253

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1253" class="line" lang="cpp">                 </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1254" 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">

1254

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1255" 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">

1255

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1255" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1256" 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">

1256

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1256" class="line" lang="cpp">                         <span class="n" style="color: #333;">getDispatcher</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iterate</span> <span class="p">(</span><span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">FillPartitions</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1257" 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">

1257

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1257" class="line" lang="cpp">                                                                                                                                                 <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_cached_items_per_core_per_part</span><span class="p">,</span> <span class="n" style="color: #333;">_progress</span><span class="p">,</span> <span class="n" style="color: #333;">_bankStats</span><span class="p">,</span> <span class="n" style="color: #333;">_tmpPartitions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_repartitor</span><span class="p">,</span> <span class="n" style="color: #333;">pInfo</span><span class="p">,</span><span class="n" style="color: #333;">_superKstorage</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1258" 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">

1258

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1258" class="line" lang="cpp">                                                                                                                                                 <span class="p">),</span> <span class="n" style="color: #333;">groupSize</span><span class="p">,</span> <span class="n" style="color: #333;">deleteSynchro</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1259" 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">

1259

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1259" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1260" 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">

1260

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1260" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1261" 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">

1261

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1261" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1262" 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">

1262

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1262" class="line" lang="cpp">                         <span class="n" style="color: #333;">getDispatcher</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iterate</span> <span class="p">(</span><span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">FillPartitions</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1263" 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">

1263

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1263" class="line" lang="cpp">                                                                                                                                                          <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_cached_items_per_core_per_part</span><span class="p">,</span> <span class="n" style="color: #333;">_progress</span><span class="p">,</span> <span class="n" style="color: #333;">_bankStats</span><span class="p">,</span> <span class="n" style="color: #333;">_tmpPartitions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_repartitor</span><span class="p">,</span> <span class="n" style="color: #333;">pInfo</span><span class="p">,</span><span class="n" style="color: #333;">_superKstorage</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1264" 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">

1264

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1264" class="line" lang="cpp">                                                                                                                                                          <span class="p">),</span> <span class="n" style="color: #333;">groupSize</span><span class="p">,</span> <span class="n" style="color: #333;">deleteSynchro</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1265" 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">

1265

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1265" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1266" 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">

1266

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1266" class="line" lang="cpp">                 </span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1267" 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">

1267

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1267" class="line" lang="cpp">                 </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1268" 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">

1268

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1268" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We flush the partitions in order to be sure to have the exact number of items per partition. */</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1269" 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">

1269

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1269" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1270" 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">

1270

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1270" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1271" 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">

1271

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1271" class="line" lang="cpp">                         <span class="n" style="color: #333;">_tmpPartitions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1272" 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">

1272

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1272" class="line" lang="cpp">                         </span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1273" 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">

1273

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1273" class="line" lang="cpp">                         <span class="cm" style="color: #998; font-style: italic;">/** We get a snapshot of items number in each partition. */</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1274" 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">

1274

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1274" class="line" lang="cpp">                         <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nbItems</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1275" 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">

1275

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1275" 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;">size_t</span> <span class="n" style="color: #333;">p</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;">p</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">;</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1276" 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">

1276

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1276" class="line" lang="cpp">                         <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1277" 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">

1277

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1277" class="line" lang="cpp">                          <span class="n" style="color: #333;">nbItems</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_tmpPartitions</span><span class="p">)[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">getNbItems</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">//todo for multi count</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1278" 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">

1278

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1278" class="line" lang="cpp">                         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1279" 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">

1279

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1279" class="line" lang="cpp">                         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1280" 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">

1280

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1280" class="line" lang="cpp">                         <span class="cm" style="color: #998; font-style: italic;">/** We add the current number of kmers in each partition for the reached ith bank. */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1281" 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">

1281

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1281" class="line" lang="cpp">                         <span class="n" style="color: #333;">_nbKmersPerPartitionPerBank</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="n" style="color: #333;">nbItems</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1282" 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">

1282

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1282" class="line" lang="cpp">                 <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1283" 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">

1283

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<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1283" class="line" lang="cpp">                 </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1284" 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">

1284

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1284" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">//GR: close the input bank here with call to finalize</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1285" 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">

1285

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1285" class="line" lang="cpp">                 <span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1286" 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">

1286

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1287" 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">

1287

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="cpp">         </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1288" 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">

1288

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1288" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_solidityKind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">KMER_SOLIDITY_SUM</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1289" 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">

1289

</td>

<td class="diff-line-num new_line old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1289" class="line" lang="cpp">         <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1236" 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">

1236

</td>

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

<pre style="margin: 0;">+<span id="LC1236" class="line" lang="cpp"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1237" 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">

1237

</td>

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

<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We fill the partitions. Each thread will read synchronously and will</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1238" 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">

1238

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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      * call FillPartitions in a synchronous way (in order to have global</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1239" 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">

1239

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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      * BanksStats correctly computed). */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1240" 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">

1240

</td>

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

<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp">                 <span class="n" style="color: #333;">getDispatcher</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iterate</span><span class="p">(</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1241" 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">

1241

</td>

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

<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp">                         <span class="n" style="color: #333;">itSeq</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1242" 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">

1242

</td>

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

<pre style="margin: 0;">+<span id="LC1242" class="line" lang="cpp">                         <span class="n" style="color: #333;">FillPartitions</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1243" 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">

1243

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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp">                             <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1244" 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">

1244

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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="cpp">                             <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_cached_items_per_core_per_part</span><span class="p">,</span> <span class="n" style="color: #333;">_progress</span><span class="p">,</span> <span class="n" style="color: #333;">_bankStats</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1245" 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="LC1245" class="line" lang="cpp">                             <span class="n" style="color: #333;">_tmpPartitions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_repartitor</span><span class="p">,</span> <span class="n" style="color: #333;">pInfo</span><span class="p">,</span> <span class="n" style="color: #333;">_superKstorage</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1246" 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">

1246

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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp">                         <span class="n" style="color: #333;">groupSize</span><span class="p">,</span> <span class="n" style="color: #333;">deleteSynchro</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1290" 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="1247" 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">

1247

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

<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1248" 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="LC1248" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// GR: close the input bank here with call to finalize</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" 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="1249" 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">

1249

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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="cpp">                 <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1250" 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">

1250

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

<pre style="margin: 0;">+<span id="LC1250" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1290

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<td class="diff-line-num new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1251

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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="cpp">                 <span class="n" style="color: #333;">_superKstorage</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flushFiles</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1291

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<td class="diff-line-num new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1252

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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="cpp">                 <span class="n" style="color: #333;">_superKstorage</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">closeFiles</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1253" 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">

1253

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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="cpp">         <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1254" 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">

1254

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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We may have several input banks instead of a single one. */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1255" 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">

1255

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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp">                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>*></span> <span class="n" style="color: #333;">itBanks</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getComposition</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1256" 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">

1256

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

<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1257" 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">

1257

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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We first reset the vector holding the kmers number for each partition and for each bank.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1258" 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">

1258

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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      * It can be seen as the following matrix:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" 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="1259" 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">

1259

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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" 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="1260" 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">

1260

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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *           part0  part1  part2 ... partJ</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1261" 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">

1261

</td>

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

<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *   bank0    xxx    xxx    xxx       xxx</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1262" 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">

1262

</td>

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

<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *   bank1    xxx    xxx    xxx       xxx</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1263" 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">

1263

</td>

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

<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *    ...</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1264" 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">

1264

</td>

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

<pre style="margin: 0;">+<span id="LC1264" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *   bankI    xxx    xxx    xxx       xxx</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1265" 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">

1265

</td>

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

<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1266" 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">

1266

</td>

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

<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      *   Here xxx is the number of items found for the bank I in the partition J</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1267" 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">

1267

</td>

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

<pre style="margin: 0;">+<span id="LC1267" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                      */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1268" 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">

1268

</td>

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

<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1269" 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">

1269

</td>

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

<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp">                 <span class="cm" style="color: #998; font-style: italic;">/** We launch the iteration of the sequences iterator with the created functors. */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1270" 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">

1270

</td>

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

<pre style="margin: 0;">+<span id="LC1270" 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;">size_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;">itBanks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1271" 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">

1271

</td>

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

<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp">                 <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1272" 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">

1272

</td>

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

<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">groupSize</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1273" 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">

1273

</td>

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

<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp">                         <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">deleteSynchro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1274" 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">

1274

</td>

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

<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1275" 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">

1275

</td>

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

<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp">                         <span class="cm" style="color: #998; font-style: italic;">/** We fill the partitions. Each thread will read synchronously and will call FillPartitions</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1276" 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">

1276

</td>

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

<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                              * in a synchronous way (in order to have global BanksStats correctly computed). */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1277" 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">

1277

</td>

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

<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1278" 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">

1278

</td>

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

<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp">                 <span class="n" style="color: #333;">getDispatcher</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iterate</span><span class="p">(</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1279" 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">

1279

</td>

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

<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp">                         <span class="n" style="color: #333;">itBanks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="1280" 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">

1280

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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp">                         <span class="n" style="color: #333;">FillPartitions</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1281" 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">

1281

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

<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp">                                 <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_passes</span><span class="p">,</span> <span class="n" style="color: #333;">pass</span><span class="p">,</span> <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1282" 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">

1282

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

<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp">                                 <span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_cached_items_per_core_per_part</span><span class="p">,</span> <span class="n" style="color: #333;">_progress</span><span class="p">,</span> <span class="n" style="color: #333;">_bankStats</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1283" 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">

1283

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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp">                                 <span class="n" style="color: #333;">_tmpPartitions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_repartitor</span><span class="p">,</span> <span class="n" style="color: #333;">pInfo</span><span class="p">,</span> <span class="n" style="color: #333;">_superKstorage</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1284" 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">

1284

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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp">                         <span class="n" style="color: #333;">groupSize</span><span class="p">,</span> <span class="n" style="color: #333;">deleteSynchro</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1285" 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">

1285

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

<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1286" 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">

1286

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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp">                         <span class="cm" style="color: #998; font-style: italic;">/** We flush the partitions in order to be sure to have the exact number of items per partition. */</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1287" 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">

1287

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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp">                                 <span class="n" style="color: #333;">_tmpPartitions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1288" 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">

1288

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

<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1289" 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">

1289

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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp">                                 <span class="cm" style="color: #998; font-style: italic;">/** We get a snapshot of items number in each partition. */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1290" 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">

1290

</td>

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

<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp">                                 <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nbItems</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1291" 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">

1291

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<pre style="margin: 0;">+<span id="LC1291" 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;">size_t</span> <span class="n" style="color: #333;">p</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;">p</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">_nb_partitions</span><span class="p">;</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1292" 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">

1292

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

<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp">                                 <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1293" 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">

1293

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

<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp">                                  <span class="n" style="color: #333;">nbItems</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_tmpPartitions</span><span class="p">)[</span><span class="n" style="color: #333;">p</span><span class="p">].</span><span class="n" style="color: #333;">getNbItems</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">//todo for multi count</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1294" 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">

1294

</td>

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

<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp">                                 <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1295" 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">

1295

</td>

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

<pre style="margin: 0;">+<span id="LC1295" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1296" 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">

1296

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

<pre style="margin: 0;">+<span id="LC1296" class="line" lang="cpp">                                 <span class="cm" style="color: #998; font-style: italic;">/** We add the current number of kmers in each partition for the reached ith bank. */</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1297" 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">

1297

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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="cpp">                                 <span class="n" style="color: #333;">_nbKmersPerPartitionPerBank</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span> <span class="p">(</span><span class="n" style="color: #333;">nbItems</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1298" 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">

1298

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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" 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="1299" 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">

1299

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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="cpp">                         <span class="c1" style="color: #998; font-style: italic;">//GR: close the input bank here with call to finalize</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" 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="1300" 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">

1300

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1292" 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="1301" 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">

1301

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1292

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<td class="diff-line-num new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1302

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1293" 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">

1293

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<td class="diff-line-num new_line old" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1293" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1294" 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">

1294

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<td class="diff-line-num new_line old" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1294" class="line" lang="cpp">         </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1295" style="width: 35px; color: rgba(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="LC1303" class="line" lang="cpp"> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1304

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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1305

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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*********************************************************************</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1424" style="width: 35px; color: rgba(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="1432" style="width: 35px; color: rgba(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">@@ -1424,8 +1432,8 @@ void SortingCountAlgorithm<span>::fillSolidKmers_aux (ICountProcessor<span>* pro</td>

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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1425" style="width: 35px; color: rgba(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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1433

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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/** If we have several input banks, we may have to compute kmer solidity for each bank, which</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1434

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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">             * can be currently done only with sorted vector. */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1427" 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="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="cpp"><span class="idiff left">            </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">forceVector</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">_nbKmersPerPartitionPerBank</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1428" 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="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1428" class="line" lang="cpp"><span class="idiff left">                                </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_solidityKind</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">KMER_SOLIDITY_SUM</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1429" 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="1435" 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="LC1435" class="line" lang="cpp"><span class="idiff left">                        </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">forceVector</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">_nbKmersPerPartitionPerBank</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_solidityKind</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">KMER_SOLIDITY_SUM</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1429" 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="LC1436" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="cpp">            <span class="n" style="color: #333;">ICommand</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cmd</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="LC1439" class="line" lang="cpp"></span>

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<li id="4c12716c6fcb516eda353ab99ab2b81002b77515">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#4c12716c6fcb516eda353ab99ab2b81002b77515"><strong>gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in</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">@@ -31,9 +31,9 @@ template void bglue<${KSIZE}>(Storage* storage,</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">template class graph3<${KSIZE}>; // graph3<span> switch  </span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">template void link_tigs<${KSIZE}></span>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>

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

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

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

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

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

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<li id="6805524260d80eecf62b8e8407368389214b1fde">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#6805524260d80eecf62b8e8407368389214b1fde"><strong>gatb-core/src/gatb/tools/collections/impl/MapMPHF.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">@@ -141,8 +141,8 @@ namespace gatb        {</td>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">                                                  </span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">                                                  </span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">                                                  </span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">UINT_MAX</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"><span class="idiff left right">                                                   </span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">                                                  <span class="n" style="color: #333;">_abundanceDiscretization</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">total</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">                                                  </span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp">                                                  </span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp">                                                  </span>

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<li id="9a3c9915f167211d4a7ca96fe03df76f04a8c369">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#9a3c9915f167211d4a7ca96fe03df76f04a8c369"><strong>gatb-core/src/gatb/tools/misc/impl/Histogram.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="85" style="width: 35px; color: rgba(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">@@ -85,6 +85,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_histogram</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_histogram_smoothed</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">        <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">_histogram2D</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IHistogram::inc */</span></span>

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<li id="4258957fbedcdb09fe6853db03d786c2be1fbc78">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#4258957fbedcdb09fe6853db03d786c2be1fbc78"><strong>gatb-core/src/gatb/tools/misc/impl/Pool.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" style="width: 35px; color: rgba(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="347" style="width: 35px; color: rgba(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">@@ -347,11 +347,9 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//clear all previous allocs, and alloc pool capacity</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">u_int64_t</span> <span class="n" style="color: #333;">size</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="349" style="width: 35px; color: rgba(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="LC349" class="line" lang="cpp">    <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">mainbuffer</span> <span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="350" 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="LC350" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mainbuffer</span> <span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

351

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351

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="352" style="width: 35px; color: rgba(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="LC352" class="line" lang="cpp">            <span class="n" style="color: #333;">FREE</span> <span class="p">(</span><span class="n" style="color: #333;">mainbuffer</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="353" 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">

353

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<td class="diff-line-num new_line old" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp">            <span class="n" style="color: #333;">capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">used_space</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="354" 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">

354

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<td class="diff-line-num new_line old" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp">            <span class="n" style="color: #333;">mainbuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

355

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<td class="diff-line-num new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

353

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="356" style="width: 35px; color: rgba(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="354" style="width: 35px; color: rgba(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="LC354" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp">        <span class="cm" style="color: #998; font-style: italic;">/** We add a little bit of memory in case "align" method is called often.</span></span>

</pre>

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<br>

</li>

<li id="440041d1ca70d3a1c65ca98b83f363a9cafd5a9e">

<a href="https://salsa.debian.org/med-team/gatb-core/commit/8febe06b31d34f7554d7dc689e1c4ecfa95d3b17#440041d1ca70d3a1c65ca98b83f363a9cafd5a9e"><strong>gatb-core/test/jenkins/test-suite-fedora20-gcc-4.8.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(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="37" style="width: 35px; color: rgba(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">@@ -37,7 +37,7 @@ JOB_NAME             : ${JOB_NAME}</td>

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37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Make sure, we use the appropriate cmake</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/home/ci-gatb/cmake-3.<span class="idiff left right">7.2</span>-Linux-x86_64/bin:<span class="nv" style="color: #008080;">$PATH</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/home/ci-gatb/cmake-3.<span class="idiff left right">10.0</span>-Linux-x86_64/bin:<span class="nv" style="color: #008080;">$PATH</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(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="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell">error_code <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DO_NOT_STOP_AT_ERROR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"true"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">return </span>0 <span class="p">;</span> <span class="o" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>

</pre>

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