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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc">b9057443</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-05-29T11:15:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.0</pre>
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</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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−
.travis.yml
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#8c2b0239da0ce709b3b1cdb4db436bd013095d6a">
data/reads_r1.fastq
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<li class="file-stats">
<a href="#229172768e5e4f16f160bb59a60f17185d66f4ec">
data/reads_r2.fastq
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<li class="file-stats">
<a href="#4634fca5c7f447885de0bf2ee2071e96ec446d2e">
data/reference.fasta
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<li class="file-stats">
<a href="#1dd61bb768b613b358467981e3d64ec6394b090d">
doc/MindTheGap_insertion_caller.md
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<li class="file-stats">
<a href="#703284c86e076b7c08d4f8b3e4ece9b08bcdfd5e">
scripts/jenkins/tool-mindthegap-build-debian7-64bits-gcc-4.7.sh
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<li class="file-stats">
<a href="#6a0b0000e222b66c4629f2dea38ece41b4232113">
scripts/jenkins/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1.sh
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<li class="file-stats">
<a href="#2ac129fec1f50dc5452a152bb54ec16bec635724">
scripts/jenkins/tool-mindthegap-release-debian.sh
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<li class="file-stats">
<a href="#742edb99d80b28555748f681b2192004565cd699">
src/FindBreakpoints.hpp
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<li class="file-stats">
<a href="#29b2c0bba706dabdd7e216e658cae5ac395d73d6">
src/FindHeteroInsertion.hpp
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<li class="file-stats">
<a href="#2cd4f140a733f1b4b5ba60b13303261892bf93aa">
src/FindSNP.hpp
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<li class="file-stats">
<a href="#2e26376367d7d6f945de0d8120af2765586832d4">
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+
src/FindSmallInsertion.hpp
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<li class="file-stats">
<a href="#5d1c61938574d188b12119e87936ce22c49407a6">
src/Finder.cpp
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<li class="file-stats">
<a href="#5a37c36ef7f6ddb7b647db8e13bf49c965fd7546">
src/Finder.hpp
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<li class="file-stats">
<a href="#906b117910dd8b40c789812570b6ea6b9c11dead">
test/full_test/README
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<li class="file-stats">
<a href="#5e5ad02fc78e3a297fa329f2f0536de7524cf3c6">
test/full_test/allele1.fasta
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<li class="file-stats">
<a href="#663bd41f08c1948bff2fd6cd5977f6a4c27c5f01">
test/full_test/allele2.fasta
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<li class="file-stats">
<a href="#eca33a54df289965fe6a85bdb8bcaffa752098b7">
test/full_test/gold.breakpoints
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<li class="file-stats">
<a href="#01e6c0095c39237a1bfc9521003f1aa9cc0fc01f">
test/full_test/gold.insertions.fasta
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<li class="file-stats">
<a href="#c8c1994bf5a622886714f298cf13c1bdff72d28c">
test/full_test/gold.insertions.vcf
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<li class="file-stats">
<a href="#b10c092b7d0dc2e98cf5cacfce65a2504da2ab6c">
test/full_test/gold.othervariants.vcf
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<li class="file-stats">
<a href="#67a55931ce6762bb201dd046914354503475d9c4">
test/full_test/gold_bed.breakpoints
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<li class="file-stats">
<a href="#4080c9c6d095c9d4cdfe76f895c2390e2965c90c">
test/full_test/gold_bed.othervariants.vcf
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<li class="file-stats">
<a href="#7b53f04776f31332bc381ffecb609a18ba6a21e2">
test/full_test/gold_fill.output
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<li class="file-stats">
<a href="#c16df07c21fdc174b1138d12fda1474cca58c93c">
test/full_test/gold_find.output
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<li class="file-stats">
<a href="#0a923f8b74d7d5281f2efcf05d27306273c4e75f">
test/full_test/reference.fasta
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
</a>
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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="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.8</span></span>
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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="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">clang-3.7</span></span>
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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="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake</span></span>
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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="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake-data</span></span>
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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="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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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="LC21" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "`echo $CXX`" == "g++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=g++-4.8; fi</span></span>
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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="LC22" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ "`echo $CXX`" == "clang++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=clang++-3.7; fi</span></span>
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23
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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="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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24
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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="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">exclude</span><span class="pi">:</span></span>
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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="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>
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27
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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="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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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="LC28" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">mkdir build</span></span>
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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="LC29" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd build</span></span>
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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="LC30" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cmake .. && make</span> </span>
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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="LC31" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">cd ../test && ./simple_full_test.sh</span></span>
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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="LC32" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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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="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">global</span><span class="pi">:</span></span>
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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="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">MAKEFLAGS="-j 4"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,16 @@</td>
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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="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Unreleased]</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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6
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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="LC6" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.3.0] - 2022-04-20</span></span>
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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="markdown"></span>
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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="markdown">Improving the <span class="sb" style="color: #d14;">`Find`</span> (insertion breakpoint finder) module:</span>
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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="markdown"></span>
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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="LC11" class="line" lang="markdown"><span class="p">*</span> very small insertions (1 or 2 bp) are now directly assembled in the <span class="sb" style="color: #d14;">`Find`</span> module and are output in the <span class="sb" style="color: #d14;">`.othervariants.vcf`</span> file. This may increase the running time of the <span class="sb" style="color: #d14;">`Find`</span> module but the overall running time of MindTheGap (Find+Fill) is drastically reduced. Indeed, these numerous small insertions are no longer output in the breakpoint file, nor given as input for the <span class="sb" style="color: #d14;">`Fill`</span> assembly module which performs a deeper traversal of the de Bruijn graph (designed for longer insertions). </span>
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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="LC12" class="line" lang="markdown"><span class="p">*</span> a novel filter is implemented to reduce the amount of False Positive insertion sites. It is based on the number of branching kmers in a 100-bp window before a heterozygous site. It can be tuned with the novel option <span class="sb" style="color: #d14;">`-branching-filter`</span>. It is now activated by default, so this may modify the amount of heterozygous sites detected with respect to previous versions. </span>
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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="LC14" class="line" lang="markdown">With this new version, the running time of MindTheGap as an insertion variant caller is reduced for real large datasets, such as human genome re-sequencing data. </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.2.3] - 2021-06-11</span></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -27,8 +27,8 @@ cmake_minimum_required(VERSION 3.1)</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The default version number is the latest official build</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MAJOR 2<span class="p">)</span></span>
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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="LC30" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR <span class="idiff left right deletion">2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC31" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right deletion">3</span><span class="p">)</span></span>
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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="LC30" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR <span class="idiff left right addition">3</span><span class="p">)</span></span>
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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="LC31" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right addition">0</span><span class="p">)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="cmake"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># But, it is possible to define another release number during a local build</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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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="markdown">| <span class="gs" style="font-weight: 600;">**Linux**</span> | <span class="gs" style="font-weight: 600;">**Mac OSX**</span> |</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">|-----------|-------------|</span>
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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="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-debian7-64bits-gcc-4.7/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-debian7-64bits-gcc-4.7/) | <span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1/)</span>
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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="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.inria.fr/gatb-core/view/MindTheGap<span class="idiff left addition">-gitlab</span>/job/tool-mindthegap-build-debian7-64bits-gcc-4.7<span class="idiff addition">-gitlab</span>/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-debian7-64bits-gcc-4.7/) | <span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.inria.fr/gatb-core/view/MindTheGap<span class="idiff addition">-gitlab</span>/job/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1<span class="idiff right addition">-gitlab</span>/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/MindTheGap/job/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1/)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/mindthegap/README.html)</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">@@ -194,27 +194,30 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"><span class="p">4.</span> <span class="gs" style="font-weight: 600;">**MindTheGap Output**</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"><span class="sb" style="color: #d14;"> All the output files are prefixed either by a default name: "MindTheGap_Expe-[date:YY:MM:DD-HH:mm]" or by a user defined prefix (option `-out` of MindTheGap).</span></span>
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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="LC197" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Both MindTheGap modules generate the graph file if reads were given as input: </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" class="line" lang="markdown"><span class="p">*</span> a graph file (<span class="sb" style="color: #d14;">`.h5`</span>). This is a binary file, to obtain information stored in it, you can use the utility program <span class="sb" style="color: #d14;">`dbginfo`</span> located in your bin directory or in ext/gatb-core/bin/.</span>
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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="LC200" class="line" lang="markdown"> </span>
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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC201" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`MindTheGap find`</span> generates the following output files:</span>
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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="LC198" class="line" lang="markdown"><span class="sb" style="color: #d14;"> The main results files are output by the Fill module, these are:</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<td class="new_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC203" class="line" lang="markdown"><span class="p"> *</span> a breakpoint file (<span class="sb" style="color: #d14;">`.breakpoints`</span>) in fasta format. </span>
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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="LC200" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * an **insertion variant file** (`.insertions.vcf`) in vcf format, in the case of insertion variant detection (for insertions >2 bp).</span></span>
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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="LC201" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC202" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * an **assembly graph file** (`.gfa`) in GFA format, in the case of contig gap-filling. It contains the original contigs and the obtained gap-fill sequences (nodes of the graph), together with their overlapping relationships (arcs of the graph).</span></span>
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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="LC203" class="line" lang="markdown"></span>
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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="LC204" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Additional output files are:</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC205" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC205" class="line" lang="markdown"><span class="p">*</span> a <span class="idiff left deletion">variant</span> file (<span class="sb" style="color: #d14;">`.<span class="idiff deletion">othervariants.vcf`</span></span><span class="idiff right deletion">) in vcf format. It contains SNPs and deletion events</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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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="LC206" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left addition"> </span>* a <span class="idiff addition">graph</span> file (`.<span class="idiff right addition">h5`), output by both MindTheGap modules. This is a binary file containing the de Bruijn graph data structure. To obtain information stored in it, you can use the utility program `dbginfo` located in your bin directory or in ext/gatb-core/bin/</span>.</span></span>
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206
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<td class="new_line diff-line-num" 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">
207
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown"><span class="p"> </span></span>
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207
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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC207" class="line" lang="markdown"> <span class="sb" style="color: #d14;"><span class="idiff left deletion">`MindTheGap fill`</span></span><span class="idiff right deletion"> generates the following output files</span>:</span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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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="LC208" class="line" lang="markdown"><span class="p"> <span class="idiff left addition">*</span></span><span class="idiff addition"> Files output specifically by </span><span class="sb" style="color: #d14;"><span class="idiff right addition">`MindTheGap find`</span></span>:</span>
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208
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<td class="new_line diff-line-num" 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">
209
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC209" class="line" lang="markdown"><span class="p"><span class="idiff left deletion">*</span></span><span class="idiff deletion"> a sequence file (</span><span class="sb" style="color: #d14;"><span class="idiff deletion">`.insertions.fasta`</span></span><span class="idiff right deletion">) in fasta format. It contains the inserted sequences or contig gap-fills that were successfully assembled</span>. </span>
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210
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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC210" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
211
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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC211" class="line" lang="markdown"><span class="p">*</span> a<span class="idiff left deletion">n insertion</span> variant file (<span class="sb" style="color: #d14;">`.<span class="idiff deletion">insertion</span>s.vcf`</span>) in vcf format<span class="idiff right deletion">, in the case of insertion variant detection. </span></span>
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<td class="old_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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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="LC210" class="line" lang="markdown"><span class="p"><span class="idiff left addition"> *</span></span><span class="idiff addition"> a breakpoint file (</span><span class="sb" style="color: #d14;"><span class="idiff addition">`.breakpoints`</span></span><span class="idiff right addition">) in fasta format</span>. </span>
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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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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="LC211" class="line" lang="markdown"><span class="p"> <span class="idiff left right addition"> </span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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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="LC212" class="line" lang="markdown"><span class="p"><span class="idiff left addition"> </span>*</span> a variant file (<span class="sb" style="color: #d14;">`.<span class="idiff addition">othervariant</span>s.vcf`</span>) in vcf format<span class="idiff right addition">. It contains SNPs, deletions and very small insertions (1-2 bp).</span></span>
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212
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<td class="new_line diff-line-num" 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">
213
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC213" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num old" 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">
213
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC213" class="line" lang="markdown"><span class="p">*</span> an assembly graph file (<span class="sb" style="color: #d14;">`.gfa`</span>) in GFA format, in the case of contig gap-filling. It contains the original contigs and the obtained gap-fill sequences (nodes of the graph), together with their overlapping relationships (arcs of the graph).</span>
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<td class="old_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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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="LC214" class="line" lang="markdown"><span class="p"> *</span> Files output specifically by <span class="sb" style="color: #d14;">`MindTheGap fill`</span>:</span>
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<td class="new_line diff-line-num new" 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">
215
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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="LC215" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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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="LC216" class="line" lang="markdown"><span class="p"> *</span> a sequence file (<span class="sb" style="color: #d14;">`.insertions.fasta`</span>) in fasta format. It contains the inserted sequences (for insertions >2 bp) or contig gap-fills that were successfully assembled. </span>
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214
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<td class="new_line diff-line-num" 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">
217
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC217" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
215
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<td class="new_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC215" class="line" lang="markdown"><span class="p">*</span> a log file (<span class="sb" style="color: #d14;">`.info.txt`</span>), a tabular file with some information about the filling process for each breakpoint/grap-fill. </span>
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<td class="old_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); 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="new_line diff-line-num new" 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">
218
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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="LC218" class="line" lang="markdown"><span class="p"><span class="idiff left right addition"> </span>*</span> a log file (<span class="sb" style="color: #d14;">`.info.txt`</span>), a tabular file with some information about the filling process for each breakpoint/grap-fill. </span>
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216
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="old_line diff-line-num old" 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">
217
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="p">*</span> with option <span class="sb" style="color: #d14;">`-extend`</span>, an additional sequence file (<span class="sb" style="color: #d14;">`.extensions.fasta`</span>) in fasta format. It contains sequence extensions for failed insertion or gap-filling assemblies, ie. when the target kmer was not found, the first contig immediately after the source kmer is output.</span>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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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="LC220" class="line" lang="markdown"><span class="p"><span class="idiff left right addition"> </span>*</span> with option <span class="sb" style="color: #d14;">`-extend`</span>, an additional sequence file (<span class="sb" style="color: #d14;">`.extensions.fasta`</span>) in fasta format. It contains sequence extensions for failed insertion or gap-filling assemblies, ie. when the target kmer was not found, the first contig immediately after the source kmer is output.</span>
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218
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221
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"> </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">@@ -233,10 +236,14 @@ Either in your `bin/` directory or in `ext/gatb-core/bin/`, you can find additio</td>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Reference</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"></span>
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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="LC239" class="line" lang="markdown">If you use MindTheGap, please cite: </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown">MindTheGap: integrated detection and assembly of short and long insertions. Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. Bioinformatics 2014 30(24):3451-3457. http://bioinformatics.oxfordjournals.org/content/30/24/3451</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC242" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Web page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gatb.inria.fr/software/mind-the-gap/</span><span class="p">)</span> with some updated results.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC245" class="line" lang="markdown">MindTheGap was also evaluated in a recent benchmark exploring many different genomic features (size, nature, repeat context, junctional homology at breakpoints) of human insertion variants. Among other tested SV callers, MindTheGap was the only tool able to output sequence-resolved insertions for many types of insertions. Read more: <span class="p">[</span><span class="nv" style="color: #008080;">Towards a better understanding of the low recall of insertion variants with short-read based variant callers.</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07125-5</span><span class="p">)</span> Delage W, Thevenon J, Lemaitre C. <span class="ge" style="font-style: italic;">*BMC Genomics*</span> <span class="gs" style="font-weight: 600;">**2020**</span>, 21(1):762.</span>
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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="LC246" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Contact</span></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#8c2b0239da0ce709b3b1cdb4db436bd013095d6a"><strong>data/reads_r1.fastq</strong></a>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#229172768e5e4f16f160bb59a60f17185d66f4ec"><strong>data/reads_r2.fastq</strong></a>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#4634fca5c7f447885de0bf2ee2071e96ec446d2e"><strong>data/reference.fasta</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>
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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">@@ -8,3 +8,7 @@ TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCG</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTAATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGCTGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAGGTATCCTTACTTTCGGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">>Seq4</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACCCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAAGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCCCGAACATTGAGACCTGGCCAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGGTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT</span>
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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="LC12" class="line" lang="plaintext">GATGTTTAGAAGTTTCCAGGTCACGCCAATGATTGGCATTTACACACGTGGATCAGCGGACATATCTAACCCTTAGTGTTCTTAAGAGCAACTCACTACTCATTTCCACTAACCCCGCCGGCGGTAATTCCAATCTAGTTGATCAGACTTCCCAGTCAATGAAAGCGACACCGTGCGTCTGTAATACCAACAAGACCCTGCTGTCGTCCCGCAGAGGACGCGGCACCTCCGGATTTTGAGTCCAGTCTGAACGATTTTCGATCACTCACCATGGATCTGGAAAACGGAGTCGAGTACTCAGAGCCAAATTGATGCATTTCCAATGACCCGATGCAGGTGCGACCGATCTTCGCCTATGCTTCCCGCCGTAATTATTGAGTCTGGGTCCCGGCCGCTAACGTTGACTCACGGGGAGGTACCCGTGCGTATTCTTCTCAAAGTGACGCTGGACAGCAGCGCATGTCCGAGCCCCATCGTCCTATCTGGTGTAGAGTCTTACCCTAATTAGAGTGATCGAACCAGTAGGTGTCGCGGTCTTAGGGCTCCCATTGTCCAAGGGAACGTGAACAGATATGAATCTGGGAGAATAGTGCAGCGTTGCCCTTCTGGTCGGTCAGCCCTTGCCTACGGCCCGTATGCGGAGAATGAAGGCGTGAAACATTCTGCTCTTTTAGAAGCAGCGGCTGCACCCGTATAACAATCGCACGATCGTACGTCTCATTTGCCGCGTTGGCGCGCCCGTGGATGATGGACCACGGTATGAACCTCTGCACTTCAAATTTGACGCAATCCTGCACTCACCGCACACAGTTCTAGTCTAACCGTCGCAGTGTCTGCTTTAAGGTAGAGATCGATACTTAGGATATGTTCATGTGTGTTTGTAGCGCTGGACCCTCTTATGGTGTGGTCACTTGTGATGGATCGAGGAACTTAGGCGGTTAACTTGTTTCGACGTCTCACCGACAATATCAGGATTTAGTATCG</span>
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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="LC13" class="line" lang="plaintext">>Seq6</span>
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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="LC14" class="line" lang="plaintext">ACCGAAAATGACAATGTTCACACGCATGCTCGGCGTGGAAAAGAGCCTTTTCTAAGACCGACTCGTTCCGGGCAGCAGGATTATTAGCCAATCAAAATTATCGACCGGTCATCAAGCTGCGATAGTGCAGGCGCATGCCGTCCAATGGGTCCACGGCGGAAGTGCGTTCGTCTACTCTGTCAAATCTTAACATTTTTTGAGGCTAATCCGGCCGGTAGTGTACCGTGAACCAAAGTCCTTCTACGAGCGTATTAGATTGCTCAAAAGATCCGGGAGAATTGACCAGGTCGTATCTTTAAAAACGCTGGTGCGAGCAGCTGCTGTTTTATCAACACCCATTTAGTCCTGTGAAGTTTGCTTAGCAGATACACCTTCCCGCGTGGTATGAGAGGCTGTTCTTTTAAAAACTATGAGGCTCTGGCACCTTCGACGCTAACAAAGTCCCCACGGACCATGATACCCTTACGCAACTCTCTTTGCACGCTAGGGCGAGAGTACTGCCCCTAGACTAGGTACACGCCGGGTAAACTCTCTCGCACACCTTTACGCTCGACTACAGGCTTCTAACCCTTCCGAACGCATATAATTCAAATGGCACTTAGTAACAGACGAATCACGGCTCACAGGCAGAATTCACTGGAGTAAAAGGATTCAGAACAATAGATAGTGTGTTAACTTTACAGTCATCCGTATTATAACGTAGCGAGAGGATTGAGTTCTTGTTAGGAAGGAAGGTCCTATAGACGAGTGCGGTAGCGCACCCGGTCGCCTTGCGTAGTCATGCCCGACGTGTTGATGGTTCCCTTTTAGCCGCCACACAAGGGATCCGAGGGTGAGAGACACATGGCCCTCACCGACGAGACTTACTCAGCCTGCCTCGCTATTGCCCTCTTTTTGATCGTCCCTTTGTGGCTCTCGAGGACTCGTGCAGCGTGTATCTGGGGATTTGTAAGCTTAAGACTACCTTCCATAGGA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#1dd61bb768b613b358467981e3d64ec6394b090d"><strong>doc/MindTheGap_insertion_caller.md</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,18 +34,28 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p">4.</span> <span class="gs" style="font-weight: 600;">**Find module specific options**</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"> In addition to the read or graph files, the <span class="sb" style="color: #d14;">`find`</span> module has one mandatory option <span class="sb" style="color: #d14;">`-ref`</span> and several optional options:</span>
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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="LC37" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-ref`</span>: the path to the reference genome file (in fasta format).</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-homo-only`</span>: only homozygous insertions are reported (default: not activated).</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-max-rep`</span>: maximal repeat size allowed for fuzzy sites [default '5']. </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-het-max-occ`</span>: maximal number of occurrences of a (k-1)mer in the reference genome allowed for heterozyguous insertion breakpoints [default '1']. In order to detect an heterozyguous insertion breakpoints, both flanking k-1-mers, at each side of the insertion site, must have strictly less than this number of occurrences in the reference genome. This prevents false positive predictions inside repeated regions. Warning : increasing this parameter may lead to numerous false positives (genomic approximate repeats).</span>
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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="LC41" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-bed`</span>: the path to a bed file defining genomic regions, to limit the find algorithm to particular regions of the genome. This can be usefull for exome data.</span>
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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="LC42" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-branching-filter`</span>: maximal number of branching kmers in a 100-bp window before a heterozygous site [default '15', '-1' means no filter applied]. This filter prevents numerous false positive predictions inside repeated regions. In large and complex genomes, such as human, this parameter can be set to lower values (10 or 5), in order to decrease the running time of the Fill module (but this may result in a loss of recall in repeat-rich regions).</span>
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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="LC43" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-bed`</span>: the path to a bed file defining genomic regions, to limit the find algorithm to particular regions of the genome. This can be usefull for exome data. Important: the bed file has to be sorted and overlapping intervals merged, such as:</span>
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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="LC46" class="line" lang="markdown"> sort -k1,1 -k2,2n file.bed > file_sorted.bed</span>
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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="LC47" class="line" lang="markdown"> bedtools merge -i file_sorted.bed > file_final.bed</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="p">5.</span> <span class="gs" style="font-weight: 600;">**Fill module specific options**</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"> </span>
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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="LC45" class="line" lang="markdown"> In addition to the read or graph files, the <span class="sb" style="color: #d14;">`fill`</span> module has one other mandatory option, <span class="sb" style="color: #d14;">`-bkpt`</span> </span>
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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC46" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-bkpt`</span>: the breakpoint file path. This is one of the output of the <span class="sb" style="color: #d14;">`find`</span> module and contains for each detected insertion site its left and right kmers from and to which the local assembly will be performed (see section E for details about the format).</span>
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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="LC53" class="line" lang="markdown"> In addition to the read or graph files, the <span class="sb" style="color: #d14;">`fill`</span> module has one other mandatory option, <span class="sb" style="color: #d14;">`-bkpt`</span>:</span>
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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="LC54" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="new_line diff-line-num new" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-bkpt`</span>: the breakpoint file path. This is one of the output of the <span class="sb" style="color: #d14;">`find`</span> module and contains for each detected insertion site its left and right kmers from and to which the local assembly will be performed (see section <span class="p">[</span><span class="nv" style="color: #008080;">Output formats</span><span class="p">](</span><span class="sx" style="color: #d14;">#output-formats</span><span class="p">)</span> for details about the format).</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"> The fill module has several optional options:</span>
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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="LC58" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-max-nodes`</span>: maximum number of nodes in contig graph for each insertion assembly [default '100']. This arguments limits the computational time, this is especially useful for complex genomes.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-max-length`</span>: maximum number of assembled nucleotides in the contig graph (nt) [default '10000']. This arguments limits the computational time, this is especially useful for complex genomes.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`-filter`</span>: if set, insertions with multiple solutions are not output in the final vcf file (default : not activated).</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">@@ -55,21 +65,25 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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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="markdown"> All the output files are prefixed either by a default name: "MindTheGap_Expe-[date:YY:MM:DD-HH:mm]" or by a user defined prefix (option <span class="sb" style="color: #d14;">`-out`</span> of MindTheGap)</span>
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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="markdown"> Both MindTheGap modules generate the graph file if reads were given as input: </span>
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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="LC68" class="line" lang="markdown"><span class="p"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="p"> *</span> a graph file (<span class="sb" style="color: #d14;">`.h5`</span>). This is a binary file, to obtain information stored in it, you can use the utility program dbginfo located in your bin directory or in ext/gatb-core/bin/.</span>
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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="markdown"> </span>
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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="markdown"> <span class="sb" style="color: #d14;">`MindTheGap find`</span> generates the following output files:</span>
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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="LC72" class="line" lang="markdown"><span class="p"> </span></span>
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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="markdown"><span class="p"> *</span> a breakpoint file (<span class="sb" style="color: #d14;">`.breakpoints`</span>) in fasta format. It contains the breakpoint sequences of each detected insertion site. Each insertion site corresponds to 2 consecutive entries in the fasta file : sequences are the left and right side flanking kmers.</span>
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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="LC62" class="line" lang="markdown"><span class="p"> *</span> a variant file (<span class="sb" style="color: #d14;">`.othervariants.vcf`</span>) in vcf format. It contains SNPs<span class="idiff left deletion"> and</span> deletion <span class="idiff right deletion">events</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC74" class="line" lang="markdown"><span class="p"> *</span> a variant file (<span class="sb" style="color: #d14;">`.othervariants.vcf`</span>) in vcf format. It contains SNPs<span class="idiff left addition">,</span> deletion <span class="idiff right addition">and very small insertions (1-2 bp)</span>.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`MindTheGap fill`</span> generates the following output files:</span>
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65
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="p"> *</span> a sequence file (<span class="sb" style="color: #d14;">`.insertions.fasta`</span>) in fasta format. It contains the inserted sequences or contig gap-fills that were successfully assembled. In the case of insertion variants, the location of each insertion on the reference genome can be found in its fasta header. The fasta header includes also information about each gap-fill such as its length, quality score and median kmer abundance.</span>
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="p"> *</span> an insertion variant file (<span class="sb" style="color: #d14;">`.insertions.vcf`</span>) in vcf format, in the case of insertion variant detection. This file contains all information of assembled insertion variants as in the <span class="sb" style="color: #d14;">`.insertions.fasta`</span> file but in a different format. Here, insertion site positions are 1-based and left-normalized according to the VCF format specifications (contrary to positions indicated in the <span class="sb" style="color: #d14;">`.breakpoints`</span> and <span class="sb" style="color: #d14;">`insertions.fasta`</span> files which are right-normalized). Normalization occurs when multiple positions are possible for a single variation due to a small repeat. </span>
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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="markdown"><span class="p"> </span></span>
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<td class="new_line diff-line-num new" 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">
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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="markdown"><span class="p"> *</span> a sequence file (<span class="sb" style="color: #d14;">`.insertions.fasta`</span>) in fasta format (for insertions >2 bp). It contains the inserted sequences or contig gap-fills that were successfully assembled. In the case of insertion variants, the location of each insertion on the reference genome can be found in its fasta header. The fasta header includes also information about each gap-fill such as its length, quality score and median kmer abundance.</span>
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<td class="new_line diff-line-num new" 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="markdown"><span class="p"> *</span> an insertion variant file (<span class="sb" style="color: #d14;">`.insertions.vcf`</span>) in vcf format (for insertions >2 bp). This file contains all information of assembled insertion variants as in the <span class="sb" style="color: #d14;">`.insertions.fasta`</span> file but in a different format. Here, insertion site positions are 1-based and left-normalized according to the VCF format specifications (contrary to positions indicated in the <span class="sb" style="color: #d14;">`.breakpoints`</span> and <span class="sb" style="color: #d14;">`insertions.fasta`</span> files which are right-normalized). Normalization occurs when multiple positions are possible for a single variation due to a small repeat. </span>
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67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="p"> *</span> a log file (<span class="sb" style="color: #d14;">`.info.txt`</span>), a tabular file with some information about the filling process for each breakpoint/grap-fill. </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Details on output formats</span></span>
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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="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"output-formats"</span><span class="nt" style="color: #000080;">></a></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"><span class="p">1.</span> Breakpoint format</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"> </span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,6 +112,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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98
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="sb" style="color: #d14;"> FILTER field: can be `PASS`or `LOWQUAL` (for insertions with multiple solutions)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;"> INFO fields: </span></span>
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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="LC115" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `TYPE`: variant type, INS for insertion</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `LEN`: insertion size in bp</span></span>
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103
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118
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `QUAL`: quality of the insertion (quality scores range from 0 to 50, 50 being the best quality, see the different quality scores [below](#quality))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +143,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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128
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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="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"quality"</span><span class="nt" style="color: #000080;">></a></span></span>
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129
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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="markdown"> </span>
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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="markdown"> Each insertion is assigned a quality score ranging from 0 (low quality) to 50 (highest quality). This quality score reflects mainly repeat-associated criteria:</span>
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146
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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="LC146" class="line" lang="markdown"><span class="p"> </span></span>
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131
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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="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`qual=5`</span>: if one of the breakpoint kmer could not be found exactly but with 2 errors (mismatches)</span>
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132
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`qual=10`</span>: if one of the breakpoint kmer could not be found exactly but with 1 error (mismatch)</span>
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133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="p"> *</span> <span class="sb" style="color: #d14;">`qual=15`</span>: if multiple sequences can be assembled for a given breakpoint (note that to output multiple sequences, they must differ from each other significantly, ie. <90% identity)</span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -137,6 +153,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>
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137
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"><span class="p">5.</span> Gap-filling information file:</span>
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138
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"></span>
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139
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"><span class="sb" style="color: #d14;"> For each gap-fill, some informations about the filling process are given in the file `.info.txt`, whether it has been successfully filled or not. This can help understand why some breakpoints could not be filled. Here are the description of the columns:</span></span>
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156
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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="LC156" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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140
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * column 1 : breakpoint name </span></span>
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141
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * column 2-4 : number of nodes in the contig graph, total nt assembled, number of nodes containing the right breakpoint kmer</span></span>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * (optionnally) column 5-7 : same informations as in column 2-4 but for the filling process in the reverse direction from right to left kmer, activated only if the filling failed in the forward direction</span></span>
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<li id="703284c86e076b7c08d4f8b3e4ece9b08bcdfd5e">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#703284c86e076b7c08d4f8b3e4ece9b08bcdfd5e"><strong>scripts/jenkins/tool-mindthegap-build-debian7-64bits-gcc-4.7.sh</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">@@ -28,6 +28,8 @@ DO_NOT_STOP_AT_ERROR : ${DO_NOT_STOP_AT_ERROR}</td>
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28
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="s2" style="color: #d14;"> Jenkins build parameters (built in)</span></span>
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29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="s2" style="color: #d14;">-----------------------------------------</span></span>
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30
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="s2" style="color: #d14;">BUILD_NUMBER : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BUILD_NUMBER</span><span class="k" style="font-weight: 600;">}</span></span>
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31
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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="LC31" class="line" lang="shell"><span class="s2" style="color: #d14;">JENKINS_HOME : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">JENKINS_HOME</span><span class="k" style="font-weight: 600;">}</span></span>
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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="s2" style="color: #d14;">WORKSPACE : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WORKSPACE</span><span class="k" style="font-weight: 600;">}</span></span>
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31
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" 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>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,12 +56,15 @@ g++ --version</td>
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54
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56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"></span>
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55
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57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="sb" style="color: #d14;">`</span>gcc <span class="nt" style="color: #000080;">-dumpversion</span><span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">=</span> 4.7 <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="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"GCC 4.7"</span><span class="p">;</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="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"GCC version is not 4.7, we exit"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span> <span class="o" style="font-weight: 600;">}</span></span>
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58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"></span>
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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="LC57" class="line" lang="shell"><span class="nv" style="color: #008080;">JENKINS_TASK</span><span class="o" style="font-weight: 600;">=</span>tool-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOOL_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-build-debian7-64bits-gcc-4</span>.7</span>
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59
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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="LC59" class="line" lang="shell"><span class="nv" style="color: #008080;">JENKINS_TASK</span><span class="o" style="font-weight: 600;">=</span>tool-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOOL_NAME</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-build-debian7-64bits-gcc-4</span>.7-gitlab</span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nv" style="color: #008080;">JENKINS_WORKSPACE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$WORKSPACE</span>/<span class="nv" style="color: #008080;">$JENKINS_TASK</span>/</span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="nv" style="color: #008080;">GIT_DIR</span><span class="o" style="font-weight: 600;">=</span>/scratchdir/builds/workspace/gatb-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOOL_NAME</span><span class="k" style="font-weight: 600;">}</span></span>
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59
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63
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="nv" style="color: #008080;">BUILD_DIR</span><span class="o" style="font-weight: 600;">=</span>/scratchdir/<span class="nv" style="color: #008080;">$JENKINS_TASK</span>/gatb-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOOL_NAME</span><span class="k" style="font-weight: 600;">}</span>/build</span>
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60
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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="shell"></span>
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61
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65
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$BUILD_DIR</span></span>
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62
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66
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$BUILD_DIR</span></span>
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67
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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="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$JENKINS_WORKSPACE</span></span>
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"></span>
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64
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-----------------------------------------------</span></span>
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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="shell"><span class="c" style="color: #998; font-style: italic;"># we need gatb-core submodule to be initialized</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,10 +123,19 @@ cd build</td>
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118
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123
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># PACKAGING #</span></span>
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119
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124
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################</span></span>
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120
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125
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC125" class="line" lang="shell"></span>
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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="LC121" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Upload bin bundle to the forge</span></span>
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126
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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="LC126" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#-- Upload bin bundle as a build artifact</span></span>
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127
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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="LC127" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># -> bin bundle *-bin-Linux.tar.gz will be archived as a build artifact</span></span>
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128
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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="LC128" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># -> source package is handled by the osx task</span></span>
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129
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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="LC129" class="line" lang="shell"></span>
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122
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130
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <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;">$INRIA_FORGE_LOGIN</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> none <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DO_NOT_STOP_AT_ERROR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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123
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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="LC123" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>make package</span>
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124
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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="LC124" class="line" lang="shell"> scp <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Linux</span>.tar.gz <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INRIA_FORGE_LOGIN</span><span class="k" style="font-weight: 600;">}</span>@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria</span>
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125
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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="LC125" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># source package is handled by the osx task</span></span>
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131
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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="LC131" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Creating a binary archive... "</span></span>
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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="shell"> make package</span>
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133
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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="LC134" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">pwd</span></span>
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135
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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="LC135" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> ls</span> <span class="nt" style="color: #000080;">-atlhrsF</span></span>
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136
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137
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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="LC137" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#-- Move the generated bin bundle to the workspace (so that it can be uploaded as a Jenkins job artifact)</span></span>
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138
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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="LC138" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv</span> <span class="k" style="font-weight: 600;">*</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Linux</span>.tar.gz <span class="nv" style="color: #008080;">$JENKINS_WORKSPACE</span>/</span>
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139
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126
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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="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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127
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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="shell"></span></pre></td>
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<li id="6a0b0000e222b66c4629f2dea38ece41b4232113">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#6a0b0000e222b66c4629f2dea38ece41b4232113"><strong>scripts/jenkins/tool-mindthegap-build-macos-10.9.5-gcc-4.2.1.sh</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,8 @@ DO_NOT_STOP_AT_ERROR : ${DO_NOT_STOP_AT_ERROR}</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="s2" style="color: #d14;"> Jenkins build parameters (built in)</span></span>
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29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="s2" style="color: #d14;">-----------------------------------------</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="s2" style="color: #d14;">BUILD_NUMBER : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BUILD_NUMBER</span><span class="k" style="font-weight: 600;">}</span></span>
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31
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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="LC31" class="line" lang="shell"><span class="s2" style="color: #d14;">JENKINS_HOME : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">JENKINS_HOME</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="s2" style="color: #d14;">WORKSPACE : </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WORKSPACE</span><span class="k" style="font-weight: 600;">}</span></span>
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33
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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35
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,9 +119,12 @@ cd ../build</td>
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117
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119
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"></span>
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118
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Prepare and upload bin and source bundle to the forge</span></span>
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119
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <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;">$INRIA_FORGE_LOGIN</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> none <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DO_NOT_STOP_AT_ERROR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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120
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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="LC120" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left right deletion"> </span></span>make package</span>
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122
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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="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left right addition"> </span></span>make package</span>
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121
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"> make package_source</span>
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122
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<td class="new_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC122" class="line" lang="shell"> scp <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Darwin</span>.tar.gz <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INRIA_FORGE_LOGIN</span><span class="k" style="font-weight: 600;">}</span>@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria</span>
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123
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<td class="new_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC123" class="line" lang="shell"> scp <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-Source</span>.tar.gz <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INRIA_FORGE_LOGIN</span><span class="k" style="font-weight: 600;">}</span>@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria</span>
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124
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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="LC124" class="line" lang="shell"></span>
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125
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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="LC125" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># make both tar.gz available as Jenkins build artifacts </span></span>
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<td class="new_line diff-line-num new" 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">
126
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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="LC126" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Darwin</span>.tar.gz <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WORKSPACE</span><span class="k" style="font-weight: 600;">}</span>/</span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-Source</span>.tar.gz <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">WORKSPACE</span><span class="k" style="font-weight: 600;">}</span>/</span>
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128
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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="LC128" class="line" lang="shell"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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125
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130
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC130" class="line" lang="shell"></span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#2ac129fec1f50dc5452a152bb54ec16bec635724"><strong>scripts/jenkins/tool-mindthegap-release-debian.sh</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">@@ -85,18 +85,24 @@ if [ "$INRIA_FORGE_LOGIN" == none ]; then</td>
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85
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85
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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86
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86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"></span>
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<td class="old_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$BUILD_DIR</span></span>
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88
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<td class="new_line diff-line-num old" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="shell">git clone https://github.com/<span class="idiff left right deletion">pgdurand</span>/github-release-api.git</span>
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<td class="new_line diff-line-num new" 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">
88
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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="LC88" class="line" lang="shell">git clone https://github.com/<span class="idiff left right addition">GATB</span>/github-release-api.git</span>
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89
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89
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"></span>
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90
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90
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################</span></span>
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91
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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># RETRIEVE ARCHIVES FROM INRIA FORGE #</span></span>
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92
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92
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################</span></span>
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93
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93
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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="shell"><span class="nv" style="color: #008080;">CI_URL</span><span class="o" style="font-weight: 600;">=</span>https://ci.inria.fr/gatb-core/view/MindTheGap-gitlab/job</span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="nv" style="color: #008080;">JENKINS_TASK_DEB</span><span class="o" style="font-weight: 600;">=</span>tool-mindthegap-build-debian7-64bits-gcc-4.7-gitlab</span>
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<td class="new_line diff-line-num new" 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="shell"><span class="nv" style="color: #008080;">JENKINS_TASK_MAC</span><span class="o" style="font-weight: 600;">=</span>tool-mindthegap-build-macos-10.9.5-gcc-4.2.1-gitlab</span>
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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="shell"></span>
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94
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#retrieve last build from ci-inria (see tool-lean-build-XXX tasks)</span></span>
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95
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<td class="new_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"><span class="idiff left deletion">scp </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">${</span></span><span class="nv" style="color: #008080;"><span class="idiff deletion">INRIA_FORGE_LOGIN</span></span><span class="k" style="font-weight: 600;"><span class="idiff deletion">}</span></span><span class="idiff deletion">@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Linux</span>.tar.gz<span class="idiff deletion"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right deletion">.</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="idiff left addition">wget </span><span class="nv" style="color: #008080;"><span class="idiff addition">$CI_URL</span></span><span class="idiff addition">/</span><span class="nv" style="color: #008080;"><span class="idiff addition">$JENKINS_TASK_DEB</span></span><span class="idiff addition">/lastSuccessfulBuild/artifact/</span><span class="nv" style="color: #008080;"><span class="idiff right addition">$JENKINS_TASK_DEB</span></span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Linux</span>.tar.gz</span>
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<td class="old_line diff-line-num" 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">
96
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC97" class="line" lang="shell">scp <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INRIA_FORGE_LOGIN</span><span class="k" style="font-weight: 600;">}</span>@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Darwin</span>.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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<td class="new_line diff-line-num new" 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="shell"></span>
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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="shell">wget <span class="nv" style="color: #008080;">$CI_URL</span>/<span class="nv" style="color: #008080;">$JENKINS_TASK_MAC</span>/lastSuccessfulBuild/artifact/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-bin-Darwin</span>.tar.gz</span>
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98
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103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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99
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<td class="new_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC99" class="line" lang="shell">scp <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INRIA_FORGE_LOGIN</span><span class="k" style="font-weight: 600;">}</span>@scm.gforge.inria.fr:/home/groups/gatb-tools/htdocs/ci-inria/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-Source</span>.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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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="shell"></span>
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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="shell">wget <span class="nv" style="color: #008080;">$CI_URL</span>/<span class="nv" style="color: #008080;">$JENKINS_TASK_MAC</span>/lastSuccessfulBuild/artifact/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ARCHIVE_NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BRANCH_TO_BUILD</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-Source</span>.tar.gz</span>
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100
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106
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC106" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="old_line diff-line-num" 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">
101
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107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="shell"></span>
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102
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108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################</span></span>
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<li id="742edb99d80b28555748f681b2192004565cd699">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#742edb99d80b28555748f681b2192004565cd699"><strong>src/FindBreakpoints.hpp</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ public :</td>
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103
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<td class="new_line diff-line-num" 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">
103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** writes a given variant in the output vcf file</span></span>
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104
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104
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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105
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105
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeVcfVariant</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bkt_id</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;">chrom_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_char</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alt_char</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">repeat_size</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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106
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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="LC106" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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 class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeIndel</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bkt_id</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;">chrom_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_char</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alt_char</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">repeat_size</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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107
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107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"></span>
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108
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108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*Getter*/</span></span>
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109
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Return the number of found breakpoints</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,7 +130,7 @@ public :</td>
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130
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130
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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131
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131
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">kmer_size</span><span class="p">();</span></span>
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132
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132
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>
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133
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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="LC133" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Return the <span class="idiff left right deletion">numbre of </span>max repeat </span></span>
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<td class="old_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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133
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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="LC133" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Return the max repeat <span class="idiff left right addition">size at breakpoint</span></span></span>
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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="cm" style="color: #998; font-style: italic;"> */</span></span>
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135
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_repeat</span><span class="p">();</span></span>
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136
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,6 +138,9 @@ public :</td>
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138
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138
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<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 class="cm" style="color: #998; font-style: italic;"> */</span></span>
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139
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">snp_min_val</span><span class="p">();</span></span>
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140
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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>
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141
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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="LC141" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Return the threashold value of the branching filter</span></span>
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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="cm" style="color: #998; font-style: italic;"> */</span></span>
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143
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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="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">branching_threshold</span><span class="p">();</span></span>
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141
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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>
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142
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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;">/** The last solid kmer before gap</span></span>
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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="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</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 +236,18 @@ public :</td>
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233
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236
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Incremente the value of backup_iterate</span></span>
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234
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237
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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="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">backup_iterate</span><span class="p">();</span></span>
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236
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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="LC236" class="line" lang="cpp"> </span>
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239
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240
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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="LC240" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*Incremente the value of homo_clean_indel</span></span>
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241
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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="LC241" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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242
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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="LC242" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">homo_clean_indel_iterate</span><span class="p">();</span></span>
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243
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244
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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="LC244" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Incremente the value of homo_fuzzy_indel</span></span>
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245
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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="LC245" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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246
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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="LC246" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">homo_fuzzy_indel_iterate</span><span class="p">();</span></span>
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247
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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="LC247" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Incremente the value of hetero_indel</span></span>
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248
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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="LC248" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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249
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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="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hetero_indel_iterate</span><span class="p">();</span></span>
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250
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251
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*Setter*/</span></span>
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238
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252
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Set value of recent_hetero</span></span>
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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 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">@@ -465,8 +479,12 @@ void FindBreakpoints<span>::operator()()</td>
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479
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">);</span></span>
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466
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480
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp"> <span class="p">}</span></span>
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467
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481
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">m_chrom_name</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// we are on the current chromosome</span></span>
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468
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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="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">interval</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;">make_pair</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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469
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<td class="new_line diff-line-num old" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">interval_vector</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">interval</span><span class="p">));</span></span>
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482
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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="LC482" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bed_begin</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
483
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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="LC483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bed_end</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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484
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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="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">bed_end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">bed_begin</span><span class="p">)</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;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_kmerSize</span><span class="p">){</span></span>
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485
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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="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">interval</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;">make_pair</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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486
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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="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">interval_vector</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">interval</span><span class="p">));</span></span>
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487
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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="LC487" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">iss</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC490" 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">@@ -489,18 +507,28 @@ void FindBreakpoints<span>::operator()()</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">end_pos</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;">interval_vector</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">());</span></span>
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508
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <span class="p">}</span></span>
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509
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> </span>
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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="LC492" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m_it_kmer</span><span class="p">).</span><span class="n" style="color: #333;">isValid</span><span class="p">()</span><span class="idiff left deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">||</span></span><span class="idiff deletion"> </span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">m_position</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="n" style="color: #333;"><span class="idiff deletion">start_pos</span></span><span class="p"><span class="idiff right deletion">)</span>)</span></span>
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510
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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="LC510" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m_it_kmer</span><span class="p">).</span><span class="n" style="color: #333;">isValid</span><span class="p">())</span></span>
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511
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"> <span class="p">{</span></span>
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494
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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="LC494" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Reintialize stretch_size for each bed region</span></span>
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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="LC495" class="line" lang="cpp"> </span>
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512
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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="LC512" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Re-initialize stretch_size</span></span>
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496
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513
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_solid_stretch_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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514
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_gap_stretch_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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498
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515
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_kmer_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KmerCanonical</span><span class="p">();</span></span>
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499
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516
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_kmer_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KmerCanonical</span><span class="p">();</span></span>
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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="LC500" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//DEBUG</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_position</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">start_pos</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;">//for each beginning of bed region</span></span>
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521
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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="LC521" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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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="LC522" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Re-initialize stretch_size for each bed region</span></span>
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523
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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="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_solid_stretch_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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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_gap_stretch_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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525
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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="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_kmer_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KmerCanonical</span><span class="p">();</span></span>
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526
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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="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_kmer_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KmerCanonical</span><span class="p">();</span></span>
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527
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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="LC527" class="line" lang="cpp"> </span>
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528
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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="LC528" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Re-initialize het_kmer_history for each bed region</span></span>
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529
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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="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</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;">m_het_kmer_history</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">info_type</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">256</span><span class="p">);</span></span>
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532
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC533" 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;">m_it_kmer</span><span class="p">).</span><span class="n" style="color: #333;">isValid</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">m_position</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">start_pos</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">//inside the current bed interval</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC534" 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">@@ -648,7 +676,30 @@ void FindBreakpoints<span>::writeVcfVariant(int bkt_id, string& chrom_name, uint</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">repeat_size</span></span>
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677
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> <span class="p">);</span></span>
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678
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"><span class="p">}</span></span>
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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="LC651" class="line" lang="cpp"></span>
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679
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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="LC679" 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>
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680
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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="LC680" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FindBreakpoints</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;">writeIndel</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bkt_id</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;">chrom_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alt_string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">repeat_size</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">type</span><span class="p">)</span></span>
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682
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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="LC682" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// NOTE : currently all positions coming from FindObservers are 0-based, VCF is supposed to be 1-based, so we add +1</span></span>
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683
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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="LC683" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variant_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt_string</span><span class="p">.</span><span class="n" style="color: #333;">length</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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684
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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="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">GT</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"./."</span><span class="p">;</span></span>
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685
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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="LC685" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"HOM"</span><span class="p">)</span></span>
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686
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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="LC686" class="line" lang="cpp"> <span class="p">{</span></span>
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687
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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="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">GT</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1/1"</span><span class="p">;</span></span>
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688
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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="LC688" class="line" lang="cpp"> <span class="p">}</span></span>
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689
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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="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"HET"</span><span class="p">)</span></span>
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690
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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="LC690" class="line" lang="cpp"> <span class="p">{</span></span>
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691
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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="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">GT</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0/1"</span><span class="p">;</span></span>
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692
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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="LC692" class="line" lang="cpp"> <span class="p">}</span></span>
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693
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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="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</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;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_vcf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lli</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bkpt%i</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PASS</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TYPE=INS;LEN=%i;FUZZY=%i</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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694
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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="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">chrom_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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695
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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="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">position</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;">//switch to 1-based</span></span>
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696
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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="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">bkt_id</span><span class="p">,</span></span>
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697
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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="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_string</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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698
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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="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">alt_string</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span></span>
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699
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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="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_size</span><span class="p">,</span></span>
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700
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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="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">repeat_size</span><span class="p">,</span></span>
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701
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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="LC701" class="line" lang="cpp"> <span class="n" style="color: #333;">GT</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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702
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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="LC702" class="line" lang="cpp"><span class="p">}</span></span>
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652
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703
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*Getter*/</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC704" 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>
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705
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FindBreakpoints</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;">node_in_branch</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;">kmer_node</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">@@ -710,6 +761,12 @@ int FindBreakpoints<span>::snp_min_val()</td>
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761
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_snp_min_val</span><span class="p">;</span></span>
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762
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"><span class="p">}</span></span>
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763
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"></span>
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764
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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="LC764" 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>
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765
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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="LC765" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FindBreakpoints</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;">branching_threshold</span><span class="p">()</span></span>
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766
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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="LC766" class="line" lang="cpp"><span class="p">{</span></span>
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767
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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="LC767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_branching_threshold</span><span class="p">;</span></span>
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768
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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="LC768" class="line" lang="cpp"><span class="p">}</span></span>
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769
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*Kmer related object*/</span></span>
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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="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>
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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;">typename</span> <span class="n" style="color: #333;">FindBreakpoints</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;">KmerCanonical</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">FindBreakpoints</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;">kmer_begin</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">@@ -870,7 +927,22 @@ int FindBreakpoints<span>::backup_iterate()</td>
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927
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"><span class="p">{</span></span>
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928
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nb_backup</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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929
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"><span class="p">}</span></span>
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930
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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="LC930" 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>
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931
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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="LC931" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FindBreakpoints</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;">homo_clean_indel_iterate</span><span class="p">()</span></span>
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932
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933
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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="LC933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nb_homo_clean_indel</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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934
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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="LC934" class="line" lang="cpp"><span class="p">}</span></span>
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873
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935
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp"></span>
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936
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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="LC936" 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>
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937
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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="LC937" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FindBreakpoints</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;">homo_fuzzy_indel_iterate</span><span class="p">()</span></span>
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938
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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="LC938" class="line" lang="cpp"><span class="p">{</span></span>
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939
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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="LC939" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nb_homo_fuzzy_indel</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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940
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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="LC940" class="line" lang="cpp"><span class="p">}</span></span>
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941
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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="LC941" 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>
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942
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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="LC942" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FindBreakpoints</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;">hetero_indel_iterate</span><span class="p">()</span></span>
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943
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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="LC943" class="line" lang="cpp"><span class="p">{</span></span>
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944
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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="LC944" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nb_hetero_indel</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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945
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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="LC945" class="line" lang="cpp"><span class="p">}</span></span>
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946
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC946" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*Setter*/</span></span>
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947
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC947" class="line" lang="cpp"><span class="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>
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948
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC948" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FindBreakpoints</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;">recent_hetero</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">value</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">@@ -29,8 +29,10 @@ template<size_t span></td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FindHeteroInsertion</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">IFindObserver</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>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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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="LC32" 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;">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;">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;">Kmer</span><span class="p">;</span></span>
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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="LC33" 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;">ModelCanonical</span> <span class="n" style="color: #333;">KmerModel</span><span class="p">;</span></span>
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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="LC34" 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;">KmerModel</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span> <span class="n" style="color: #333;">KmerIterator</span><span class="p">;</span></span>
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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="LC35" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">FindHeteroInsertion</span><span class="p">(</span><span class="n" style="color: #333;">FindBreakpoints</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;">find</span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" 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">@@ -47,12 +49,24 @@ bool FindHeteroInsertion<span>::update()</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homo_only</span><span class="p">())</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="p">{</span></span>
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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="LC52" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// branching filter parameters</span></span>
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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="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">branching_threshold</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">branching_threshold</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">//max number of branching kmers in the 100 bp window of previous kmers</span></span>
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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="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_branching_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">branching_threshold</span><span class="p">;</span></span>
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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="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filtering</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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56
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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="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">branching_threshold</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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57
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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="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">filtering</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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">max_branching_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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59
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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="LC59" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">filter_window_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span> <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//should not be larger than the size of het_kmer_history = 256</span></span>
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62
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// hetero site detection</span></span>
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51
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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 class="k" style="font-weight: 600;">if</span><span class="p">(</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end_is_repeated</span><span class="p">()</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_info</span><span class="p">().</span><span class="n" style="color: #333;">nb_in</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="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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</span><span class="p">())</span></span>
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52
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65
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="p">{</span></span>
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53
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<td class="new_line diff-line-num" 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 class="c1" style="color: #998; font-style: italic;">//loop over putative repeat size (0=clean, >0 fuzzy), reports only the smallest repeat size found.</span></span>
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54
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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;">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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_repeat</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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55
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found_base_one</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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56
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<td class="new_line diff-line-num" 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 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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_begin_index</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">nb_out</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="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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_begin_index</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">is_repeated</span><span class="p">)</span></span>
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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="p">{</span></span>
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58
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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="c1" style="color: #998; font-style: italic;">//hetero breakpoint found</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,32 +74,102 @@ bool FindHeteroInsertion<span>::update()</td>
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60
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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 class="c1" style="color: #998; font-style: italic;">//string kmer_end_str = this->_find->model().toString(this->_find->current_info().kmer);</span></span>
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61
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<td class="new_line diff-line-num" 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">
75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//modif 15/06/2018 to check !!! (before in case of fuzzy>0, the end and right kmers overlapped, => insertion of wrong size (- fuzzy), missing the repeat + loss of recall if insertion of size < repeat)</span></span>
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62
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76
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer_end_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_seq</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]),</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">());</span></span>
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63
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC63" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</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;">codeSeed</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_seq</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">]),</span><span class="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;">isValid</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">kmer_begin_str</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;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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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>
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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;">//Tests if this can be a small (1-2 bp) insertion</span></span>
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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="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TT"</span><span class="p">};</span></span>
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<td class="new_line diff-line-num new" 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;">KmerModel</span> <span class="n" style="color: #333;">local_m</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">KmerIterator</span> <span class="n" style="color: #333;">local_it</span><span class="p">(</span><span class="n" style="color: #333;">local_m</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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;">string</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</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;">codeSeed</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_seq</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">]),</span><span class="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;">isValid</span><span class="p">())</span></span>
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64
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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">{</span></span>
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65
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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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66
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<td class="new_line diff-line-num" 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">
88
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="p">}</span></span>
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67
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<td class="new_line diff-line-num old" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeBreakpoint</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_name</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_end_str</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">STR_HET_TYPE</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_begin_index</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">is_repeated</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end_is_repeated</span><span class="p">()</span> <span class="p">);</span></span>
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68
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<td class="new_line diff-line-num old" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> </span>
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69
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<td class="new_line diff-line-num old" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id_iterate</span><span class="p">();</span></span>
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70
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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="LC70" class="line" lang="cpp"> </span>
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71
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<td class="new_line diff-line-num old" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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89
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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="LC89" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" 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;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</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;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// for all possible 1-2 bp insertions, perform a micro-assembly</span></span>
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72
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="p">{</span></span>
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73
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<td class="new_line diff-line-num old" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hetero_clean_iterate</span><span class="p">();</span></span>
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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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_begin_str</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kmer_end_str</span><span class="p">;</span></span>
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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="n" style="color: #333;">Data</span> <span class="n" style="color: #333;">local_d</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</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="new_line diff-line-num new" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_valid</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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95
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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="LC95" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// // Init this variable</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">local_d</span><span class="p">.</span><span class="n" style="color: #333;">setRef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">setData</span><span class="p">(</span><span class="n" style="color: #333;">local_d</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">local_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;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>
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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 class="p">{</span></span>
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100
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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="LC100" 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;">contains</span><span class="p">(</span><span class="n" style="color: #333;">local_it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forward</span><span class="p">()))</span></span>
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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="p">{</span></span>
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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="n" style="color: #333;">sum_valid</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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="p">}</span></span>
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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="k" style="font-weight: 600;">else</span></span>
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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 class="p">{</span></span>
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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 class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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107
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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="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sum_valid</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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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="LC109" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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">
110
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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="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">inser_base_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">found_base_one</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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112
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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="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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113
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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="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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114
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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="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">found_base_one</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span></span>
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115
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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="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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116
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">else</span></span></span>
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117
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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="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">if</span></span><span class="idiff addition"> </span><span class="p"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">found_base_one</span></span><span class="p"><span class="idiff right addition">)</span></span></span>
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118
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hetero_fuzzy_iterate</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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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="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeIndel</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_name</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">STR_HET_TYPE</span><span class="p">);</span></span>
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120
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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="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hetero_indel_iterate</span><span class="p">();</span></span>
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121
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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="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id_iterate</span><span class="p">();</span></span>
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122
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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="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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123
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC79" class="line" lang="cpp"> </span>
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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="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_repeat</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// we found a breakpoint, the next hetero one mus be at least _max_repeat apart from this one.</span></span>
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<td class="old_line diff-line-num old" 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="new_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//reports only the smallest repeat size found.</span></span>
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124
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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="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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125
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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="LC125" class="line" lang="cpp"> <span class="p">{</span></span>
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126
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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="LC126" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" 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">
127
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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="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//this may be a large insertion</span></span>
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128
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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="LC128" class="line" lang="cpp"> </span>
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129
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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="LC129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_branching</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="new_line diff-line-num new" 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">
130
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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="LC130" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Applying the branching-filter :</span></span>
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<td class="new_line diff-line-num new" 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">
131
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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="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filtering</span><span class="p">){</span></span>
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<td class="new_line diff-line-num new" 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 class="c1" style="color: #998; font-style: italic;">//counts the number of branching-kmers among the 100 previous ones</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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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="LC133" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_prev</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="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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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="LC134" 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="n" style="color: #333;">begin_index</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_begin_index</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="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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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="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">nb_branching</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">max_branching_kmers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">nb_prev</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filter_window_size</span><span class="p">)){</span></span>
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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;">//cout << "in loop" << nb_prev << " " << begin_index-nb_prev << endl;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" 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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</span><span class="p">(</span><span class="n" style="color: #333;">begin_index</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nb_prev</span><span class="p">).</span><span class="n" style="color: #333;">nb_out</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</span><span class="p">(</span><span class="n" style="color: #333;">begin_index</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nb_prev</span><span class="p">).</span><span class="n" style="color: #333;">nb_in</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="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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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="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">nb_branching</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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139
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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="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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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="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">nb_prev</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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141
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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="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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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="p">}</span></span>
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143
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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="LC143" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nb_branching</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">max_branching_kmers</span><span class="p">){</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeBreakpoint</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_name</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">i</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_end_str</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">STR_HET_TYPE</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_begin_index</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">is_repeated</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end_is_repeated</span><span class="p">());</span></span>
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146
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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="LC146" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" 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">
147
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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="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id_iterate</span><span class="p">();</span></span>
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148
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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="LC148" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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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="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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150
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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="LC150" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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">
151
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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="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hetero_clean_iterate</span><span class="p">();</span></span>
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152
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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="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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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="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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154
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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="LC154" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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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="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hetero_fuzzy_iterate</span><span class="p">();</span></span>
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156
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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="LC156" class="line" lang="cpp"> <span class="p">}</span></span>
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157
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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="LC157" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" 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">
158
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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="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_repeat</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">// we found a breakpoint, the next hetero one mus be at least _max_repeat apart from this one.</span></span>
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<td class="new_line diff-line-num new" 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">
159
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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="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//reports only the smallest repeat size found.</span></span>
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160
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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="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" 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">
161
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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="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// stop the loop over fuzzy size, because the branching context will remain not good for other fuzzy sizes</span></span>
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162
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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="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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;">// when recent_hetero=0 : we are sufficiently far from the previous hetero-site</span></span>
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163
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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="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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164
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165
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82
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166
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="p">}</span></span>
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83
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167
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="p">}</span></span>
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168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC85" class="line" lang="cpp"><span class="idiff left right deletion"> </span></span>
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86
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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="idiff left right deletion"> </span><span class="c1" style="color: #998; font-style: italic;">// when recent_hetero=0 : we are sufficiently far from the previous hetero-site</span></span>
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169
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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="LC169" class="line" lang="cpp"></span>
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170
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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="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recent_hetero</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;">// when recent_hetero=0 : we are sufficiently far from the previous hetero-site</span></span>
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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 class="p">}</span></span>
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172
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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="LC172" class="line" lang="cpp"></span>
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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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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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>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#2cd4f140a733f1b4b5ba60b13303261892bf93aa"><strong>src/FindSNP.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">@@ -146,9 +146,7 @@ bool FindSNP<span>::snp_at_end(unsigned char* beginpos, size_t limit, KmerType*</td>
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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="n" style="color: #333;">nuc</span><span class="p">[</span><span class="n" style="color: #333;">un</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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147
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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="n" style="color: #333;">nuc</span><span class="p">[</span><span class="n" style="color: #333;">deux</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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148
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148
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">nuc</span><span class="p">[</span><span class="n" style="color: #333;">trois</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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149
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150
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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="LC150" 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="n" style="color: #333;">endpos</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;">beginpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">limit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">256</span><span class="p">;</span></span>
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151
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" 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="n" style="color: #333;">beginpos_init</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;">beginpos</span><span class="p">);</span></span>
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153
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151
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//this->remove_nuc(nuc, *beginpos);</span></span>
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154
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_nuc</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">het_kmer_history</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">beginpos</span><span class="p">).</span><span class="n" style="color: #333;">kmer</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;">// obtain the reference nuc</span></span>
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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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* MindTheGap: Integrated detection and assembly of insertion variants</span></span>
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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="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* Authors: C. Lemaitre, G. Rizk, P. Marijon, W. Delage</span></span>
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6
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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="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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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="cpp"><span class="cm" style="color: #998; font-style: italic;">* This program is free software: you can redistribute it and/or modify</span></span>
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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="cpp"><span class="cm" style="color: #998; font-style: italic;">* it under the terms of the GNU Affero General Public License as</span></span>
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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="cpp"><span class="cm" style="color: #998; font-style: italic;">* published by the Free Software Foundation, either version 3 of the</span></span>
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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="cpp"><span class="cm" style="color: #998; font-style: italic;">* License, or (at your option) any later version.</span></span>
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11
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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="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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12
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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="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* This program is distributed in the hope that it will be useful,</span></span>
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13
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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="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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14
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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="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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15
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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="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* GNU Affero General Public License for more details.</span></span>
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16
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17
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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="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* You should have received a copy of the GNU Affero General Public License</span></span>
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18
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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="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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19
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20
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21
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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="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef FINDSMALLINSERTION_HPP_</span></span>
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22
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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="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define FINDSMALLINSERTION_HPP_</span></span>
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23
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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="LC23" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//**********************************</span></span>
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24
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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="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <IFindObserver.hpp></span></span>
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25
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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="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FindBreakpoints.hpp></span></span>
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26
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27
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28
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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="LC28" 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>
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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="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FindSmallCleanInsertion</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">IFindObserver</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>
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31
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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="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" 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;">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;">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;">Kmer</span><span class="p">;</span></span>
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34
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35
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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="LC35" 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;">ModelCanonical</span> <span class="n" style="color: #333;">KmerModel</span><span class="p">;</span></span>
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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="LC36" 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;">KmerModel</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span> <span class="n" style="color: #333;">KmerIterator</span><span class="p">;</span></span>
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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="LC40" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver<span></span></span>
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41
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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="LC42" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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43
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44
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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="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">FindSmallCleanInsertion</span><span class="p">(</span><span class="n" style="color: #333;">FindBreakpoints</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;">find</span><span class="p">);</span></span>
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45
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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="LC47" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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48
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49
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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="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">update</span><span class="p">();</span></span>
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50
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51
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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="LC52" 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>
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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="LC53" class="line" lang="cpp"><span class="n" style="color: #333;">FindSmallCleanInsertion</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;">FindSmallCleanInsertion</span><span class="p">(</span><span class="n" style="color: #333;">FindBreakpoints</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;">find</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">IFindObserver</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;">find</span><span class="p">){}</span></span>
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54
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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="LC54" class="line" lang="cpp"></span>
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55
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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="LC55" 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>
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56
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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="LC56" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">FindSmallCleanInsertion</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;">update</span><span class="p">()</span></span>
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57
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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="LC57" class="line" lang="cpp"><span class="p">{</span></span>
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58
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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="LC58" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_begin</span><span class="p">().</span><span class="n" style="color: #333;">isValid</span><span class="p">()</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end</span><span class="p">().</span><span class="n" style="color: #333;">isValid</span><span class="p">())</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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60
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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="LC60" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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">
61
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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="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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62
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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="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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63
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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="LC63" class="line" lang="cpp"></span>
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64
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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="LC64" 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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gap_stretch_size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_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;">//Check size of gap</span></span>
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65
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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="LC65" class="line" lang="cpp"> <span class="p">{</span></span>
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66
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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="LC66" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// obtains the kmer sequence</span></span>
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<td class="new_line diff-line-num new" 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">
67
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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="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer_begin_str</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;">_find</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;">toString</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_begin</span><span class="p">().</span><span class="n" style="color: #333;">forward</span><span class="p">());</span></span>
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68
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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="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer_end_str</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;">_find</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;">toString</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end</span><span class="p">().</span><span class="n" style="color: #333;">forward</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" 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;">string</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">kmer_begin_str</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="mi" style="color: #099;">1</span><span class="p">);</span></span>
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70
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71
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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="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//All possible insertions of size 1 and 2</span></span>
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72
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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="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span><span class="s" style="color: #d14;">"G"</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span><span class="s" style="color: #d14;">"AA"</span><span class="p">,</span><span class="s" style="color: #d14;">"AC"</span><span class="p">,</span><span class="s" style="color: #d14;">"AG"</span><span class="p">,</span><span class="s" style="color: #d14;">"AT"</span><span class="p">,</span><span class="s" style="color: #d14;">"CA"</span><span class="p">,</span><span class="s" style="color: #d14;">"CC"</span><span class="p">,</span><span class="s" style="color: #d14;">"CG"</span><span class="p">,</span><span class="s" style="color: #d14;">"CT"</span><span class="p">,</span><span class="s" style="color: #d14;">"GA"</span><span class="p">,</span><span class="s" style="color: #d14;">"GC"</span><span class="p">,</span><span class="s" style="color: #d14;">"GG"</span><span class="p">,</span><span class="s" style="color: #d14;">"GT"</span><span class="p">,</span><span class="s" style="color: #d14;">"TA"</span><span class="p">,</span><span class="s" style="color: #d14;">"TC"</span><span class="p">,</span><span class="s" style="color: #d14;">"TG"</span><span class="p">,</span><span class="s" style="color: #d14;">"TT"</span><span class="p">};</span></span>
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73
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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="LC73" class="line" lang="cpp"></span>
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74
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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="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerModel</span> <span class="n" style="color: #333;">local_m</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">());</span></span>
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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="n" style="color: #333;">KmerIterator</span> <span class="n" style="color: #333;">local_it</span><span class="p">(</span><span class="n" style="color: #333;">local_m</span><span class="p">);</span></span>
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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="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;">seq</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">string</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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;">found_base_one</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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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>
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<td class="new_line diff-line-num new" 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="c1" style="color: #998; font-style: italic;">//Test all possible insertions, by performing a micro-guided-assembly, ie. checks if all kmers of the insertion are present in the graph</span></span>
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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="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="mi" style="color: #099;">20</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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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="p">{</span></span>
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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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nucleo</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;">kmer_end_str</span><span class="p">;</span></span>
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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;">Data</span> <span class="n" style="color: #333;">local_d</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_valid</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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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="c1" style="color: #998; font-style: italic;">// Init this variable</span></span>
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87
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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 class="n" style="color: #333;">local_d</span><span class="p">.</span><span class="n" style="color: #333;">setRef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>
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88
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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="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">setData</span><span class="p">(</span><span class="n" style="color: #333;">local_d</span><span class="p">);</span></span>
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89
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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="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">local_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;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>
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91
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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="LC91" 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;">contains</span><span class="p">(</span><span class="n" style="color: #333;">local_it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forward</span><span class="p">()))</span></span>
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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="p">{</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">sum_valid</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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>
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95
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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="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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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="p">{</span></span>
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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;">break</span><span class="p">;</span></span>
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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>
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<td class="new_line diff-line-num new" 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 class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sum_valid</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">())</span></span>
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100
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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="LC100" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">inser_base_one</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" 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="n" style="color: #333;">found_base_one</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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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="p">}</span></span>
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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>
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<td class="new_line diff-line-num new" 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 class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">found_base_one</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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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 class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found_base_one</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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108
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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="LC108" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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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="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeIndel</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_name</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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 class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">STR_HOM_TYPE</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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">
110
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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="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homo_clean_indel_iterate</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id_iterate</span><span class="p">();</span></span>
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112
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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="LC112" class="line" lang="cpp"> </span>
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113
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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="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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114
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115
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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="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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116
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117
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118
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119
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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="LC119" 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>
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120
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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="LC120" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FindSmallFuzzyInsertion</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">IFindObserver</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>
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121
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122
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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="LC122" class="line" lang="cpp"><span class="k" style="font-weight: 600;">public</span> <span class="o" style="font-weight: 600;">:</span></span>
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123
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124
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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="LC124" 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;">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;">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;">Kmer</span><span class="p">;</span></span>
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125
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126
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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="LC126" 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;">ModelCanonical</span> <span class="n" style="color: #333;">KmerModel</span><span class="p">;</span></span>
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127
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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="LC127" 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;">KmerModel</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span> <span class="n" style="color: #333;">KmerIterator</span><span class="p">;</span></span>
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128
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129
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130
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131
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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="LC131" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver<span></span></span>
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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 class="cm" style="color: #998; font-style: italic;"> */</span></span>
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133
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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="LC133" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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134
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135
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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="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">FindSmallFuzzyInsertion</span><span class="p">(</span><span class="n" style="color: #333;">FindBreakpoints</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;">find</span><span class="p">);</span></span>
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136
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137
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138
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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="LC138" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** \copydoc IFindObserver::IFindObserver</span></span>
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139
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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="LC139" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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140
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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="LC140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">update</span><span class="p">();</span></span>
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141
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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="LC141" class="line" lang="cpp"><span class="p">};</span></span>
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142
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143
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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="LC143" 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>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="n" style="color: #333;">FindSmallFuzzyInsertion</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;">FindSmallFuzzyInsertion</span><span class="p">(</span><span class="n" style="color: #333;">FindBreakpoints</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;">find</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">IFindObserver</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;">find</span><span class="p">){}</span></span>
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145
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146
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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="LC146" 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>
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<td class="new_line diff-line-num new" 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">
147
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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="LC147" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">FindSmallFuzzyInsertion</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;">update</span><span class="p">()</span></span>
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148
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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="LC148" class="line" lang="cpp"><span class="p">{</span></span>
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149
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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="LC149" 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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_begin</span><span class="p">().</span><span class="n" style="color: #333;">isValid</span><span class="p">()</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end</span><span class="p">().</span><span class="n" style="color: #333;">isValid</span><span class="p">())</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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150
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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="LC150" class="line" lang="cpp"> <span class="p">{</span></span>
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151
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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="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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152
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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="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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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="LC154" 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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gap_stretch_size</span><span class="p">()</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gap_stretch_size</span><span class="p">()</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_repeat</span><span class="p">())</span></span>
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155
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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="LC155" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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">
156
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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="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">repeat_size</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gap_stretch_size</span><span class="p">();</span></span>
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157
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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="LC157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// obtains the kmer sequence</span></span>
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<td class="new_line diff-line-num new" 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">
158
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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="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer_begin_str</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;">_find</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;">toString</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_begin</span><span class="p">().</span><span class="n" style="color: #333;">forward</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" 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">
159
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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="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">kmer_end_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_seq</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">repeat_size</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" 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">
160
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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="LC160" 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;">nb_out_branch</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_begin</span><span class="p">().</span><span class="n" style="color: #333;">forward</span><span class="p">())</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</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;">nb_in_branch</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_end</span><span class="p">().</span><span class="n" style="color: #333;">forward</span><span class="p">())</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</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;">codeSeed</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_seq</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">repeat_size</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;">isValid</span><span class="p">()))</span></span>
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161
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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="LC161" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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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="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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163
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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="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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164
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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="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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165
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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="LC165" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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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="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_begin_str</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">kmer_begin_str</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;">repeat_size</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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167
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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="LC167" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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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="LC168" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//All possible insertions of size 1 and 2</span></span>
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<td class="new_line diff-line-num new" 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">
169
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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="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="mi" style="color: #099;">20</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span><span class="s" style="color: #d14;">"G"</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span><span class="s" style="color: #d14;">"AA"</span><span class="p">,</span><span class="s" style="color: #d14;">"AC"</span><span class="p">,</span><span class="s" style="color: #d14;">"AG"</span><span class="p">,</span><span class="s" style="color: #d14;">"AT"</span><span class="p">,</span><span class="s" style="color: #d14;">"CA"</span><span class="p">,</span><span class="s" style="color: #d14;">"CC"</span><span class="p">,</span><span class="s" style="color: #d14;">"CG"</span><span class="p">,</span><span class="s" style="color: #d14;">"CT"</span><span class="p">,</span><span class="s" style="color: #d14;">"GA"</span><span class="p">,</span><span class="s" style="color: #d14;">"GC"</span><span class="p">,</span><span class="s" style="color: #d14;">"GG"</span><span class="p">,</span><span class="s" style="color: #d14;">"GT"</span><span class="p">,</span><span class="s" style="color: #d14;">"TA"</span><span class="p">,</span><span class="s" style="color: #d14;">"TC"</span><span class="p">,</span><span class="s" style="color: #d14;">"TG"</span><span class="p">,</span><span class="s" style="color: #d14;">"TT"</span><span class="p">};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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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="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerModel</span> <span class="n" style="color: #333;">local_m</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">());</span></span>
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171
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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="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerIterator</span> <span class="n" style="color: #333;">local_it</span><span class="p">(</span><span class="n" style="color: #333;">local_m</span><span class="p">);</span></span>
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172
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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="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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173
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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="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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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="LC174" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found_base_one</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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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="c1" style="color: #998; font-style: italic;">//std::list<char> fourth (nucleo, nucleo + sizeof(nucleo) / sizeof(char) );</span></span>
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176
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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="LC176" 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="mi" style="color: #099;">20</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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177
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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="LC177" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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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="LC178" 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;">kmer_begin_str</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nucleo</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;">kmer_end_str</span><span class="p">;</span></span>
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179
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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="LC179" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << seq << endl;</span></span>
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180
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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="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">Data</span> <span class="n" style="color: #333;">local_d</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()));</span></span>
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181
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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="LC181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum_valid</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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182
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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="LC182" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// // Init this variable</span></span>
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183
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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="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">local_d</span><span class="p">.</span><span class="n" style="color: #333;">setRef</span><span class="p">(</span><span class="k" style="font-weight: 600;">const_cast</span><span class="o" style="font-weight: 600;"><</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>
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184
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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="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">setData</span><span class="p">(</span><span class="n" style="color: #333;">local_d</span><span class="p">);</span></span>
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185
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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="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">local_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;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">local_it</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>
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186
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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="LC186" class="line" lang="cpp"> <span class="p">{</span></span>
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187
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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="LC187" 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;">contains</span><span class="p">(</span><span class="n" style="color: #333;">local_it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">forward</span><span class="p">()))</span></span>
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188
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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="LC188" class="line" lang="cpp"> <span class="p">{</span></span>
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189
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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="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_valid</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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190
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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="LC190" class="line" lang="cpp"> <span class="p">}</span></span>
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191
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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="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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192
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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="LC192" class="line" lang="cpp"> <span class="p">{</span></span>
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193
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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="LC193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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194
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195
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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="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sum_valid</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmer_size</span><span class="p">())</span></span>
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196
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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="LC196" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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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="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">inser_base_one</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nucleo</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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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="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">found_base_one</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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199
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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="LC199" class="line" lang="cpp"> <span class="p">}</span></span>
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200
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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="LC200" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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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="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">found_base_one</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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202
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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="LC202" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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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="LC203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found_base_one</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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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="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeIndel</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_name</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;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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 class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">inser_base_one</span><span class="p">,</span> <span class="n" style="color: #333;">repeat_size</span><span class="p">,</span> <span class="n" style="color: #333;">STR_HOM_TYPE</span><span class="p">);</span></span>
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205
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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="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homo_clean_indel_iterate</span><span class="p">();</span></span>
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206
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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="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_find</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">breakpoint_id_iterate</span><span class="p">();</span></span>
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207
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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="LC207" class="line" lang="cpp"></span>
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208
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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="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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209
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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="LC209" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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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="LC210" class="line" lang="cpp"> <span class="p">}</span></span>
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211
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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="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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212
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213
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214
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215
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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="LC215" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // FINDSMALLINSERTION_HPP_</span></span>
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216
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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">@@ -27,6 +27,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FindInsertion.hpp></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FindSNP.hpp></span></span>
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29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits> //for std::numeric_limits</span></span>
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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="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FindSmallInsertion.hpp></span></span>
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31
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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32
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define PRINT_DEBUG</span></span>
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33
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" 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">@@ -63,6 +64,7 @@ Finder::Finder () : Tool ("MindTheGap find")</td>
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63
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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 class="n" style="color: #333;">_max_repeat</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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64
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65
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">_het_max_occ</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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65
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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 class="n" style="color: #333;">_snp_min_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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67
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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="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">_branching_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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66
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">_nbCores</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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67
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69
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">_breakpoint_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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68
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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 class="n" style="color: #333;">_vcf_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -75,14 +77,17 @@ Finder::Finder () : Tool ("MindTheGap find")</td>
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75
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">_nb_solo_snp</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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76
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">_nb_multi_snp</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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77
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79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">_nb_backup</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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" 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;">_nb_homo_clean_indel</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="new_line diff-line-num new" 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;">_nb_homo_fuzzy_indel</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="new_line diff-line-num new" 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="n" style="color: #333;">_nb_hetero_indel</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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79
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83
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">_homo_only</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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80
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84
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">_homo_insert</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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81
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85
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">_hete_insert</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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82
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86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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83
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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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84
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88
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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85
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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="LC85" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<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 class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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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>
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">_bed_file_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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87
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92
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> </span>
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93
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">setHelp</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">HelpFinder</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,6 +117,7 @@ Finder::Finder () : Tool ("MindTheGap find")</td>
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112
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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
117
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">finderParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_INSERT_ONLY</span><span class="p">,</span> <span class="s" style="color: #d14;">"search only insertion breakpoints (do not report other variants)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>
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113
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118
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//finderParser->getParser(STR_INSERT_ONLY)->setVisible(false);</span></span>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">finderParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_HET_MAX_OCC</span><span class="p">,</span> <span class="s" style="color: #d14;">"maximal number of occurrences of a kmer in the reference genome allowed for heterozyguous breakpoints"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="s" style="color: #d14;">"1"</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" 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">
120
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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="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">finderParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_BRANCHING_FILTER</span><span class="p">,</span> <span class="s" style="color: #d14;">"branching filter paramater for heterozygous insertions, maximal number of branching kmers in a 100-bp window before a heterozygous site (if -1 = no filter)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="s" style="color: #d14;">"15"</span><span class="p">));</span></span>
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115
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121
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//allow to find heterozyguous breakpoints in n-repeated regions of the reference genome</span></span>
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116
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">finderParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_MAX_REPEAT</span><span class="p">,</span> <span class="s" style="color: #d14;">"maximal repeat size detected for fuzzy sites"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"5"</span><span class="p">));</span></span>
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117
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">finderParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionNoParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_HOMO_ONLY</span><span class="p">,</span> <span class="s" style="color: #d14;">"search only homozygous breakpoints"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -305,7 +311,8 @@ void Finder::execute ()</td>
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305
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<td class="new_line diff-line-num" 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">
311
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">_max_repeat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_MAX_REPEAT</span><span class="p">);</span></span>
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306
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312
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">_het_max_occ</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_HET_MAX_OCC</span><span class="p">);</span></span>
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307
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313
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp_min_val</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_SNP_MIN_VAL</span><span class="p">);</span></span>
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308
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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="LC308" class="line" lang="cpp"></span>
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314
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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="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">_branching_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getInt</span><span class="p">(</span><span class="n" style="color: #333;">STR_BRANCHING_FILTER</span><span class="p">);</span></span>
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315
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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="LC315" class="line" lang="cpp"> </span>
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309
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316
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_het_max_occ</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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310
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317
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">_het_max_occ</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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311
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318
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC318" 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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,6 +325,7 @@ void Finder::execute ()</td>
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318
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325
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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319
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326
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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320
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327
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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328
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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="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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321
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329
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="p">}</span></span>
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330
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> </span>
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331
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_INSERT_ONLY</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -328,6 +336,7 @@ void Finder::execute ()</td>
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328
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336
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</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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329
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337
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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330
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338
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</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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339
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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="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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331
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"></span>
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342
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_SNP_ONLY</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -338,6 +347,7 @@ void Finder::execute ()</td>
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338
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347
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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339
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348
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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340
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349
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</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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350
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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="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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341
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351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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352
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"></span>
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343
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353
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_DELETION_ONLY</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); 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="358" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -348,6 +358,7 @@ void Finder::execute ()</td>
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348
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358
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</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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349
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359
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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350
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360
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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361
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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="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="p">}</span></span>
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352
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363
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"></span>
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364
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_HETERO_ONLY</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); 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="369" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -358,6 +369,7 @@ void Finder::execute ()</td>
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358
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369
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">_snp</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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359
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370
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">_backup</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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360
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371
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">_deletion</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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">_small_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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361
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"></span>
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375
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_WITH_BACKUP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -419,6 +431,10 @@ void Finder::resumeParameters(){</td>
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419
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431
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"Graph"</span><span class="p">,</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_GRAPH</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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420
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432
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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421
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433
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"Reference"</span><span class="p">,</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_REF</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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434
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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="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">STR_BED</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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435
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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="LC435" class="line" lang="cpp"> <span class="p">{</span></span>
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436
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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="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"Bed file"</span><span class="p">,</span><span class="n" style="color: #333;">_bed_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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437
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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="LC437" class="line" lang="cpp"> <span class="p">}</span></span>
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438
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="s" style="color: #d14;">"Graph"</span><span class="p">);</span></span>
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423
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439
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"kmer-size"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_kmerSize</span><span class="p">);</span></span>
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424
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440
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -456,6 +472,7 @@ void Finder::resumeParameters(){</td>
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472
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="s" style="color: #d14;">"Breakpoint detection options"</span><span class="p">);</span></span>
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457
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473
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"max_repeat"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_max_repeat</span><span class="p">);</span></span>
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458
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474
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"hetero_max_occ"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_het_max_occ</span><span class="p">);</span></span>
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475
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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="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"branching filter value"</span><span class="p">,</span> <span class="s" style="color: #d14;">"‰i"</span><span class="p">,</span> <span class="n" style="color: #333;">_branching_threshold</span><span class="p">);</span></span>
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459
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476
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"homo_insertions"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">_homo_insert</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"yes"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"no"</span><span class="p">);</span></span>
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477
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"hete_insertions"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">_hete_insert</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"yes"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"no"</span><span class="p">);</span></span>
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478
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"snp"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">_snp</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"yes"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"no"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -474,6 +491,8 @@ void Finder::resumeResults(double seconds){</td>
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474
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491
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="s" style="color: #d14;">"fuzzy"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_hetero_fuzzy</span><span class="p">);</span></span>
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475
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<td class="new_line diff-line-num" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
492
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="s" style="color: #d14;">"Other variants"</span><span class="p">);</span></span>
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476
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"deletions"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_clean_deletion</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">_nb_fuzzy_deletion</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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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="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"Homozygous insertions 1-2 bp size"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_homo_clean_indel</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_nb_homo_fuzzy_indel</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
495
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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="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"Heterozygous insertions 1-2 bp size"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_hetero_indel</span><span class="p">);</span></span>
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477
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496
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//getInfo()->add(3,"clean", "%i", _nb_clean_deletion);</span></span>
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478
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497
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//getInfo()->add(3,"fuzzy", "%i", _nb_fuzzy_deletion);</span></span>
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479
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498
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="s" style="color: #d14;">"SNPs"</span><span class="p">,</span><span class="s" style="color: #d14;">"%i"</span><span class="p">,</span> <span class="n" style="color: #333;">_nb_solo_snp</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">_nb_multi_snp</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -540,8 +559,12 @@ void Finder::runFindBreakpoints<span>::operator () (Finder* object)</td>
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540
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559
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"> <span class="p">{</span></span>
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541
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560
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">findBreakpoints</span><span class="p">.</span><span class="n" style="color: #333;">addGapObserver</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FindDeletion</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">findBreakpoints</span><span class="p">));</span></span>
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561
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp"> <span class="p">}</span></span>
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543
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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="LC543" class="line" lang="cpp"> </span>
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544
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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="LC544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_homo_insert</span><span class="p">)</span></span>
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562
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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="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_small_homo</span><span class="p">)</span></span>
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563
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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="LC563" class="line" lang="cpp"> <span class="p">{</span></span>
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564
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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="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">findBreakpoints</span><span class="p">.</span><span class="n" style="color: #333;">addGapObserver</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FindSmallCleanInsertion</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">findBreakpoints</span><span class="p">));</span></span>
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565
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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="LC565" class="line" lang="cpp"> <span class="n" style="color: #333;">findBreakpoints</span><span class="p">.</span><span class="n" style="color: #333;">addGapObserver</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FindSmallFuzzyInsertion</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">findBreakpoints</span><span class="p">));</span></span>
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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="LC566" class="line" lang="cpp"> <span class="p">}</span></span>
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567
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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="LC567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_homo_insert</span><span class="p">)</span></span>
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568
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="p">{</span></span>
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546
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569
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">findBreakpoints</span><span class="p">.</span><span class="n" style="color: #333;">addGapObserver</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FindCleanInsertion</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">findBreakpoints</span><span class="p">));</span></span>
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547
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570
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">findBreakpoints</span><span class="p">.</span><span class="n" style="color: #333;">addGapObserver</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FindFuzzyInsertion</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">findBreakpoints</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#5a37c36ef7f6ddb7b647db8e13bf49c965fd7546"><strong>src/Finder.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">@@ -31,6 +31,7 @@ static const char* STR_URI_REF = "-ref";</td>
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31
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_MAX_REPEAT</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-max-rep"</span><span class="p">;;</span></span>
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32
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32
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_HET_MAX_OCC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-het-max-occ"</span><span class="p">;</span></span>
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33
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33
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_SNP_MIN_VAL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-snp-min-val"</span><span class="p">;</span></span>
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34
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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="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_BRANCHING_FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-branching-filter"</span><span class="p">;</span></span>
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34
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35
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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35
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36
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_HOMO_ONLY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-homo-only"</span><span class="p">;</span></span>
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36
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37
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_INSERT_ONLY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-insert-only"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -65,10 +66,12 @@ public:</td>
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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 class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_mtg_version</span><span class="p">;</span></span>
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66
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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="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_kmerSize</span><span class="p">;</span></span>
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67
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">Graph</span> <span class="n" style="color: #333;">_graph</span><span class="p">;</span></span>
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Graph _ref_graph; // no longer used</span></span>
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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>
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70
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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="LC70" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//parameters</span></span>
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69
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_max_repeat</span><span class="p">;</span></span>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_het_max_occ</span><span class="p">;</span></span>
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71
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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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_snp_min_val</span><span class="p">;</span></span>
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74
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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="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_branching_threshold</span><span class="p">;</span></span>
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72
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75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nbCores</span><span class="p">;</span></span>
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76
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_homo_only</span><span class="p">;</span></span>
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74
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_homo_insert</span><span class="p">;</span></span>
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<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">@@ -76,6 +79,10 @@ public:</td>
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79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_snp</span><span class="p">;</span></span>
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77
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80
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_backup</span><span class="p">;</span></span>
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78
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81
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">_deletion</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_small_homo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_small_hetero</span><span class="p">;</span></span>
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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>
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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="c1" style="color: #998; font-style: italic;">//input/output files</span></span>
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79
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86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">IBank</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_refBank</span><span class="p">;</span></span>
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80
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87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_breakpoint_file_name</span><span class="p">;</span></span>
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81
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88
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_breakpoint_file</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,6 +91,7 @@ public:</td>
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84
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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85
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92
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_bed_file_name</span><span class="p">;</span></span>
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86
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93
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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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="c1" style="color: #998; font-style: italic;">//results statistics</span></span>
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87
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95
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_homo_clean</span><span class="p">;</span></span>
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88
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96
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_homo_fuzzy</span><span class="p">;</span></span>
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89
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97
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_hetero_clean</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,7 +101,9 @@ public:</td>
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101
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_solo_snp</span><span class="p">;</span></span>
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102
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_multi_snp</span><span class="p">;</span></span>
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103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_backup</span><span class="p">;</span></span>
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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="LC96" class="line" lang="cpp"></span>
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_homo_clean_indel</span><span class="p">;</span></span>
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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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_homo_fuzzy_indel</span><span class="p">;</span></span>
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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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_nb_hetero_indel</span><span class="p">;</span></span>
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107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Actual job done by the tool is here</span></span>
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98
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108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">execute</span> <span class="p">();</span></span>
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99
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109
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.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">@@ -26,7 +26,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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27
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" 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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28
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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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="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MTG_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right deletion">2.3</span>"</span><span class="p">;</span></span>
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29
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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="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MTG_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right addition">3.0</span>"</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_FIND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"find"</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">STR_FILL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fill"</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#906b117910dd8b40c789812570b6ea6b9c11dead"><strong>test/full_test/README</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">@@ -121,5 +121,46 @@ cp reference.fasta ../../data/reference.fasta</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"># 7. Create Gold files for automated tests</span>
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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="LC124" class="line" lang="plaintext">../../build/bin/MindTheGap find -in ../../data/reads_r1.fastq,../../data/reads_r2.fastq -ref ../../data/reference.fasta -out gold > gold_find.output</span>
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125
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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="LC125" class="line" lang="plaintext">../../build/bin/MindTheGap fill -graph gold.h5 -bkpt gold.breakpoints -out gold > gold_fill.output</span></pre></td>
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124
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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="LC124" class="line" lang="plaintext">../../build/bin/MindTheGap find -in ../../data/reads_r1.fastq,../../data/reads_r2.fastq -ref ../../data/reference.fasta -out gold -nb-cores 1 > gold_find.output</span>
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125
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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="LC125" class="line" lang="plaintext">../../build/bin/MindTheGap fill -graph gold.h5 -bkpt gold.breakpoints -out gold -nb-cores 1 > gold_fill.output</span>
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126
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127
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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="LC127" class="line" lang="plaintext"></span>
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128
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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="LC128" class="line" lang="plaintext"># 08/02/2022 : rajoute des petites insertions 1-2 bp </span>
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129
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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="LC129" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" 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">
130
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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="LC130" class="line" lang="plaintext">ou ajout de seq5 et seq6 depuis : Projets/mindTheGap/test-small-indels (990 premiers nt de chr1 et chr2, 6/10 HOM, 4/10 HET seulement dans allele 1)</span>
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131
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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="LC131" class="line" lang="plaintext"></span>
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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="plaintext"># change les param de simulation des reads : augmente couverture (+diminue tx erreurs)</span>
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133
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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="LC133" class="line" lang="plaintext">~/Bin/samtools-0.1.18/misc/wgsim -e 0.001 -d 200 -s 20 -N 1000 -1 100 -2 100 -r 0 -R 0 allele1.fasta allele1_r1.fq allele1_r2.fq</span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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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="LC134" class="line" lang="plaintext">~/Bin/samtools-0.1.18/misc/wgsim -e 0.001 -d 200 -s 20 -N 1000 -1 100 -2 100 -r 0 -R 0 allele2.fasta allele2_r1.fq allele2_r2.fq</span>
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135
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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="plaintext">cat allele1_r1.fq allele2_r1.fq > reads_r1.fastq</span>
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137
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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="LC137" class="line" lang="plaintext">cat allele1_r2.fq allele2_r2.fq > reads_r2.fastq</span>
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138
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139
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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="LC139" class="line" lang="plaintext">ATTENTION : changements dans les résultats : othervariants.vcf : perd 2 snps (Seq1 206, 219), gagne 1 del (Seq0 297) mais en perd une autre (Seq1 740) ; ne change pas les résultats des grandes insertions</span>
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140
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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="LC140" class="line" lang="plaintext"></span>
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141
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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="LC141" class="line" lang="plaintext">RQ : rate 2 petites insertions de taille 2 (Seq6 : pos 500 et 900)</span>
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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="plaintext"></span>
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143
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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="LC143" class="line" lang="plaintext"># List of all mutations :</span>
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144
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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="LC144" class="line" lang="plaintext">Seq0 101</span>
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145
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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="LC145" class="line" lang="plaintext">Seq0 123</span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Seq0 816</span>
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<td class="new_line diff-line-num new" 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">
147
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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="LC147" class="line" lang="plaintext">Seq1 206</span>
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<td class="new_line diff-line-num new" 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">
148
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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="LC148" class="line" lang="plaintext">Seq1 219</span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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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="LC149" class="line" lang="plaintext">Seq1 342</span>
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150
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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="LC150" class="line" lang="plaintext">Seq1 740</span>
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<td class="new_line diff-line-num new" 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">
151
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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="LC151" class="line" lang="plaintext">Seq2 320</span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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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="LC152" class="line" lang="plaintext">Seq2 344</span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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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="LC153" class="line" lang="plaintext">Seq2 379</span>
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154
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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="LC154" class="line" lang="plaintext">Seq2 535</span>
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155
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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="LC155" class="line" lang="plaintext">Seq2 834</span>
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<td class="old_line diff-line-num new" 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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156
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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="LC156" class="line" lang="plaintext">Seq3 256</span>
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157
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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="LC157" class="line" lang="plaintext">Seq3 511</span>
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158
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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="LC158" class="line" lang="plaintext">Seq3 766</span>
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159
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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="LC159" class="line" lang="plaintext">Seq3 781</span>
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160
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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="LC160" class="line" lang="plaintext">Seq4 257</span>
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161
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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="LC161" class="line" lang="plaintext">Seq4 349</span>
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162
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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="LC162" class="line" lang="plaintext">Seq4 512</span>
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163
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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="LC163" class="line" lang="plaintext">Seq4 600</span>
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164
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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="LC164" class="line" lang="plaintext">Seq4 841</span>
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165
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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="LC165" class="line" lang="plaintext">Seq4 884</span>
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166
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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="LC166" class="line" lang="plaintext">Seq4 821</span></pre></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">\ No newline at end of file</td>
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<li id="5e5ad02fc78e3a297fa329f2f0536de7524cf3c6">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#5e5ad02fc78e3a297fa329f2f0536de7524cf3c6"><strong>test/full_test/allele1.fasta</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">@@ -8,3 +8,7 @@ TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCG</td>
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8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTTATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGATGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAAGTATCCTTACTTTCGTTTGCAGCACTAGCCGTTCCTTGACATCTGCGGCCAACTTGTGCCTGAACCTGGAGTTTCGACAGCGTGGCGCTCTGGCCTAGTTCTTCGCTGGCACCTGGAAGAGCCGCCGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC</span>
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9
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">>Seq4</span>
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10
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACTCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAGGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGTGTATTCCTGGGTTGAGTGGCAGGTTTCTCTTAATTCTTCCCTAAGTAGCTCCGAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCGGATGGCGGCCGGAGAGCGCTGCAATCGCATGGCTCGGGACCGAACATTGAGACCTGGCTAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT</span>
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11
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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="LC11" class="line" lang="plaintext">>Seq5</span>
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<td class="old_line diff-line-num new" 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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12
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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="LC12" class="line" lang="plaintext">GATGTTTAGAAGTTTCCAGGTCACGCCAATGATTGGCATTTACACACGTGGATCAGCGGACATATCTAACCCTTAGTGTTCTTAAGAGCAACTCACTACTCCATTTCCACTAACCCCGCCGGCGGTAATTCCAATCTAGTTGATCAGACTTCCCAGTCAATGAAAGCGACACCGTGCGTCTGTAATACCAACAAGACCCTGGCTGTCGTCCCGCAGAGGACGCGGCACCTCCGGATTTTGAGTCCAGTCTGAACGATTTTCGATCACTCACCATGGATCTGGAAAACGGAGTCGAGTACTCACGAGCCAAATTGATGCATTTCCAATGACCCGATGCAGGTGCGACCGATCTTCGCCTATGCTTCCCGCCGTAATTATTGAGTCTGGGTCCCGGCCGCTAACGTTTGACTCACGGGGAGGTACCCGTGCGTATTCTTCTCAAAGTGACGCTGGACAGCAGCGCATGTCCGAGCCCCATCGTCCTATCTGGTGTAGAGTCTTACCTCTAATTAGAGTGATCGAACCAGTAGGTGTCGCGGTCTTAGGGCTCCCATTGTCCAAGGGAACGTGAACAGATATGAATCTGGGAGAATAGTGCAGCGTTGACCCTTCTGGTCGGTCAGCCCTTGCCTACGGCCCGTATGCGGAGAATGAAGGCGTGAAACATTCTGCTCTTTTAGAAGCAGCGGCTGCACCCGTATAACAACTCGCACGATCGTACGTCTCATTTGCCGCGTTGGCGCGCCCGTGGATGATGGACCACGGTATGAACCTCTGCACTTCAAATTTGACGCAATCCTGCACTCACCCGCACACAGTTCTAGTCTAACCGTCGCAGTGTCTGCTTTAAGGTAGAGATCGATACTTAGGATATGTTCATGTGTGTTTGTAGCGCTGGACCCTCTTATGGGTGTGGTCACTTGTGATGGATCGAGGAACTTAGGCGGTTAACTTGTTTCGACGTCTCACCGACAATATCAGGATTTAGTATCG</span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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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="LC13" class="line" lang="plaintext">>Seq6</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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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="LC14" class="line" lang="plaintext">ACCGAAAATGACAATGTTCACACGCATGCTCGGCGTGGAAAAGAGCCTTTTCTAAGACCGACTCGTTCCGGGCAGCAGGATTATTAGCCAATCAAAATTATATCGACCGGTCATCAAGCTGCGATAGTGCAGGCGCATGCCGTCCAATGGGTCCACGGCGGAAGTGCGTTCGTCTACTCTGTCAAATCTTAACATTTTTTGAGCGGCTAATCCGGCCGGTAGTGTACCGTGAACCAAAGTCCTTCTACGAGCGTATTAGATTGCTCAAAAGATCCGGGAGAATTGACCAGGTCGTATCTTTAAAATAACGCTGGTGCGAGCAGCTGCTGTTTTATCAACACCCATTTAGTCCTGTGAAGTTTGCTTAGCAGATACACCTTCCCGCGTGGTATGAGAGGCTGTTCTTCATTAAAAACTATGAGGCTCTGGCACCTTCGACGCTAACAAAGTCCCCACGGACCATGATACCCTTACGCAACTCTCTTTGCACGCTAGGGCGAGAGTACTGTCCCCCTAGACTAGGTACACGCCGGGTAAACTCTCTCGCACACCTTTACGCTCGACTACAGGCTTCTAACCCTTCCGAACGCATATAATTCAAATGGCACTTCAAGTAACAGACGAATCACGGCTCACAGGCAGAATTCACTGGAGTAAAAGGATTCAGAACAATAGATAGTGTGTTAACTTTACAGTCATCCGTATTATAACGTGTAGCGAGAGGATTGAGTTCTTGTTAGGAAGGAAGGTCCTATAGACGAGTGCGGTAGCGCACCCGGTCGCCTTGCGTAGTCATGCCCGACGTGTTGATGGTGGTCCCTTTTAGCCGCCACACAAGGGATCCGAGGGTGAGAGACACATGGCCCTCACCGACGAGACTTACTCAGCCTGCCTCGCTATTGCCCTCTTTTTGATCACGTCCCTTTGTGGCTCTCGAGGACTCGTGCAGCGTGTATCTGGGGATTTGTAAGCTTAAGACTACCTTCCATAGGA</span></pre></td>
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<li id="663bd41f08c1948bff2fd6cd5977f6a4c27c5f01">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#663bd41f08c1948bff2fd6cd5977f6a4c27c5f01"><strong>test/full_test/allele2.fasta</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">@@ -8,3 +8,7 @@ TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCG</td>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTTATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGATGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAAGTATCCTTACTTTCGTTTGCAGCACTAGCCGTTCCTTGACATCTGCGGCCAACTTGTGCCTGAACCTGGAGTTTCGACAGCGTGGCGCTCTGGCCTAGTTCTTCGCTGGCACCTGGAAGAGCCGCCGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC</span>
</pre></td>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">>Seq4</span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACTCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAGTCTTAACCTTAAGACCGTTCATTGATAAAACTTGCTCACGCTCTAGATGGCGTGAAGCGAAACCTAGGAAAAAGTTTTGCAGATAATTAGATTATGCGCGATACTCCGCCGTGTGTTCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAGGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGTGTATTCCTGGGTTGAGTGGCAGGTTTCTCTTAATTCTTCCCTAAGTAGCTCCGAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCGGATGGCGGCCGGAGAGCGCTGCAATCGCATGGCTCGGGACCGAACATTGAGACCTGGCTAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT</span>
</pre></td>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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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="LC11" class="line" lang="plaintext">>Seq5</span>
</pre></td>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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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="LC12" class="line" lang="plaintext">GATGTTTAGAAGTTTCCAGGTCACGCCAATGATTGGCATTTACACACGTGGATCAGCGGACATATCTAACCCTTAGTGTTCTTAAGAGCAACTCACTACTCCATTTCCACTAACCCCGCCGGCGGTAATTCCAATCTAGTTGATCAGACTTCCCAGTCAATGAAAGCGACACCGTGCGTCTGTAATACCAACAAGACCCTGGCTGTCGTCCCGCAGAGGACGCGGCACCTCCGGATTTTGAGTCCAGTCTGAACGATTTTCGATCACTCACCATGGATCTGGAAAACGGAGTCGAGTACTCACGAGCCAAATTGATGCATTTCCAATGACCCGATGCAGGTGCGACCGATCTTCGCCTATGCTTCCCGCCGTAATTATTGAGTCTGGGTCCCGGCCGCTAACGTTTGACTCACGGGGAGGTACCCGTGCGTATTCTTCTCAAAGTGACGCTGGACAGCAGCGCATGTCCGAGCCCCATCGTCCTATCTGGTGTAGAGTCTTACCTCTAATTAGAGTGATCGAACCAGTAGGTGTCGCGGTCTTAGGGCTCCCATTGTCCAAGGGAACGTGAACAGATATGAATCTGGGAGAATAGTGCAGCGTTGCCCTTCTGGTCGGTCAGCCCTTGCCTACGGCCCGTATGCGGAGAATGAAGGCGTGAAACATTCTGCTCTTTTAGAAGCAGCGGCTGCACCCGTATAACAATCGCACGATCGTACGTCTCATTTGCCGCGTTGGCGCGCCCGTGGATGATGGACCACGGTATGAACCTCTGCACTTCAAATTTGACGCAATCCTGCACTCACCGCACACAGTTCTAGTCTAACCGTCGCAGTGTCTGCTTTAAGGTAGAGATCGATACTTAGGATATGTTCATGTGTGTTTGTAGCGCTGGACCCTCTTATGGTGTGGTCACTTGTGATGGATCGAGGAACTTAGGCGGTTAACTTGTTTCGACGTCTCACCGACAATATCAGGATTTAGTATCG</span>
</pre></td>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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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="LC13" class="line" lang="plaintext">>Seq6</span>
</pre></td>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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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="LC14" class="line" lang="plaintext">ACCGAAAATGACAATGTTCACACGCATGCTCGGCGTGGAAAAGAGCCTTTTCTAAGACCGACTCGTTCCGGGCAGCAGGATTATTAGCCAATCAAAATTATATCGACCGGTCATCAAGCTGCGATAGTGCAGGCGCATGCCGTCCAATGGGTCCACGGCGGAAGTGCGTTCGTCTACTCTGTCAAATCTTAACATTTTTTGAGCGGCTAATCCGGCCGGTAGTGTACCGTGAACCAAAGTCCTTCTACGAGCGTATTAGATTGCTCAAAAGATCCGGGAGAATTGACCAGGTCGTATCTTTAAAATAACGCTGGTGCGAGCAGCTGCTGTTTTATCAACACCCATTTAGTCCTGTGAAGTTTGCTTAGCAGATACACCTTCCCGCGTGGTATGAGAGGCTGTTCTTCATTAAAAACTATGAGGCTCTGGCACCTTCGACGCTAACAAAGTCCCCACGGACCATGATACCCTTACGCAACTCTCTTTGCACGCTAGGGCGAGAGTACTGTCCCCCTAGACTAGGTACACGCCGGGTAAACTCTCTCGCACACCTTTACGCTCGACTACAGGCTTCTAACCCTTCCGAACGCATATAATTCAAATGGCACTTAGTAACAGACGAATCACGGCTCACAGGCAGAATTCACTGGAGTAAAAGGATTCAGAACAATAGATAGTGTGTTAACTTTACAGTCATCCGTATTATAACGTAGCGAGAGGATTGAGTTCTTGTTAGGAAGGAAGGTCCTATAGACGAGTGCGGTAGCGCACCCGGTCGCCTTGCGTAGTCATGCCCGACGTGTTGATGGTTCCCTTTTAGCCGCCACACAAGGGATCCGAGGGTGAGAGACACATGGCCCTCACCGACGAGACTTACTCAGCCTGCCTCGCTATTGCCCTCTTTTTGATCGTCCCTTTGTGGCTCTCGAGGACTCGTGCAGCGTGTATCTGGGGATTTGTAAGCTTAAGACTACCTTCCATAGGA</span></pre></td>
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<li id="eca33a54df289965fe6a85bdb8bcaffa752098b7">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#eca33a54df289965fe6a85bdb8bcaffa752098b7"><strong>test/full_test/gold.breakpoints</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,31 +2,31 @@</td>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="plaintext">CTCCGGATCTCCGTGTTCTTCGGAAGCTTAG</span>
</pre></td>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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="plaintext">>bkpt2_Seq0_pos_123_fuzzy_0_HET right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">GTCACGCGCGTCATACTACAGTAAGTTACTG</span>
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">6</span>_Seq1_pos_342_fuzzy_0_HET left_kmer</span>
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">5</span>_Seq1_pos_342_fuzzy_0_HET left_kmer</span>
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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">GCCGCGCAAAGCCGGTCAACAGCGTTAGTAT</span>
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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="LC7" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">6</span>_Seq1_pos_342_fuzzy_0_HET right_kmer</span>
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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">>bkpt<span class="idiff left right addition">5</span>_Seq1_pos_342_fuzzy_0_HET right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">GTTGAAAGTTTACTCAGATCGCTTCTGTCGG</span>
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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="LC9" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">11</span>_Seq2_pos_535_fuzzy_0_HOM left_kmer</span>
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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">>bkpt<span class="idiff left right addition">9</span>_Seq2_pos_535_fuzzy_0_HOM left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">GGCATGCGTAAGTTATCGTGAAACCATGATG</span>
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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="LC11" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">11</span>_Seq2_pos_535_fuzzy_0_HOM right_kmer</span>
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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="LC11" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">9</span>_Seq2_pos_535_fuzzy_0_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">GCCCCTTACTAGACCAAATGTACTGAATGCG</span>
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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="LC13" class="line" lang="plaintext">>bkpt1<span class="idiff left right deletion">2</span>_Seq2_pos_835_fuzzy_1_HOM left_kmer</span>
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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="LC13" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">0</span>_Seq2_pos_835_fuzzy_1_HOM left_kmer</span>
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">GAGCTACCCGCCCTCGGTGAGAAGGTAGTAT</span>
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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="LC15" class="line" lang="plaintext">>bkpt1<span class="idiff left right deletion">2</span>_Seq2_pos_835_fuzzy_1_HOM right_kmer</span>
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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="LC15" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">0</span>_Seq2_pos_835_fuzzy_1_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">ACCCAAACGCGTCCTATGCAGTTTTGGGCTT</span>
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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="LC17" class="line" lang="plaintext">>bkpt1<span class="idiff left right deletion">6</span>_Seq3_pos_781_fuzzy_0_HOM left_kmer</span>
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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="LC17" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">4</span>_Seq3_pos_781_fuzzy_0_HOM left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">CGGCCCATGGGAACAAGTATCCTTACTTTCG</span>
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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="LC19" class="line" lang="plaintext">>bkpt1<span class="idiff left right deletion">6</span>_Seq3_pos_781_fuzzy_0_HOM right_kmer</span>
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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="LC19" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">4</span>_Seq3_pos_781_fuzzy_0_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">GTACAAATGAGGCTCCAAAATAGCACGCTTG</span>
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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="LC21" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">6</span>_Seq4_pos_351_fuzzy_2_HET left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">GTAATCGAGATTCTCCACCATAACCTGCGCA</span>
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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="LC23" class="line" lang="plaintext">>bkpt1<span class="idiff left right addition">6</span>_Seq4_pos_351_fuzzy_2_HET right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">ATGCATCGTGAAGCTTTACCGCGCCCAAGGG</span>
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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="LC25" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">18</span>_Seq4_pos_603_fuzzy_3_HOM left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">CTTTTGGGTGCGCAACATTGCTATACTTAGG</span>
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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="LC27" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">18</span>_Seq4_pos_603_fuzzy_3_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">ATCCATTGACATCTGTCAGCCGTCTTTCCAG</span>
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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="LC29" class="line" lang="plaintext">>bkpt2<span class="idiff left right addition">0</span>_Seq4_pos_821_fuzzy_0_HOM left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">AGCGCGCTAAATTACCGCTACGAGCCATACC</span>
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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="LC31" class="line" lang="plaintext">>bkpt2<span class="idiff left right deletion">2</span>_Seq4_pos_821_fuzzy_0_HOM right_kmer</span>
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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="LC31" class="line" lang="plaintext">>bkpt2<span class="idiff left right addition">0</span>_Seq4_pos_821_fuzzy_0_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">CCGAACATTGAGACCTGGCTAGTAGGTAGGT</span></pre></td>
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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="LC1" class="line" lang="plaintext">>bkpt2_Seq0_pos_123_fuzzy_0_HET_len_137_qual_50_avg_cov_<span class="idiff left deletion">8.38</span>_median_cov_<span class="idiff right deletion">8</span>.00 </span>
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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="LC1" class="line" lang="plaintext">>bkpt2_Seq0_pos_123_fuzzy_0_HET_len_137_qual_50_avg_cov_<span class="idiff left addition">21.59</span>_median_cov_<span class="idiff right addition">21</span>.00 </span>
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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="plaintext">ATCTAAGCTGTGACCTTGTGGCCGAGGCGCTTTTCACGCCTACATTAACTCCTGGGAAGCTCTCTGCTCTAGTTTCAGTGCACATCTCCAGGTGAGCAACCCTGGCAAGCAGCCCCTTCCTGTAGAAATTACTTAGC</span>
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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="LC3" class="line" lang="plaintext">>bkpt<span class="idiff left deletion">6</span>_Seq1_pos_342_fuzzy_0_HET_len_125_qual_50_avg_cov_<span class="idiff deletion">9.91</span>_median_cov_<span class="idiff right deletion">9</span>.00 </span>
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3
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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="LC3" class="line" lang="plaintext">>bkpt<span class="idiff left addition">5</span>_Seq1_pos_342_fuzzy_0_HET_len_125_qual_50_avg_cov_<span class="idiff addition">25.17</span>_median_cov_<span class="idiff right addition">24</span>.00 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">ATGGTTTATAGAACCCGGGCGTTCATGTCCGTCAGAACGATCTTGGCACGGTAGCCCCTGGTCCAGAGAGCCAAGGTGACTCAGCCCCACGATGGTGGTCTAGAGCGAAATAACCCTCGCCGAGA</span>
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left deletion">11</span>_Seq2_pos_535_fuzzy_0_HOM_len_140_qual_50_avg_cov_<span class="idiff deletion">2</span>1.6<span class="idiff deletion">3</span>_median_cov_<span class="idiff right deletion">22</span>.00 </span>
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left addition">9</span>_Seq2_pos_535_fuzzy_0_HOM_len_140_qual_50_avg_cov_<span class="idiff addition">4</span>1.6<span class="idiff addition">6</span>_median_cov_<span class="idiff right addition">43</span>.00 </span>
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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">TAACGTTCGCTGAACATCGACTCCGGTGACGACATACGATTCAAGAAGAGAGTGACTCTGTAGGATAACATCCCGCAACGCCTAATCCATCCAGCCTGGCACCATGTATAAAGGGCGTCAGGTATGTTAACGAGACTATT</span>
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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="LC7" class="line" lang="plaintext">>bkpt1<span class="idiff left deletion">2</span>_Seq2_pos_835_fuzzy_1_HOM_len_207_qual_50_avg_cov_<span class="idiff deletion">16.50</span>_median_cov_<span class="idiff right deletion">16</span>.00 </span>
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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">>bkpt1<span class="idiff left addition">0</span>_Seq2_pos_835_fuzzy_1_HOM_len_207_qual_50_avg_cov_<span class="idiff addition">40.42</span>_median_cov_<span class="idiff right addition">42</span>.00 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">GCACGCTGCAGGATTGGAACCACAATGTACGCCGATCCAAGCAGTAGTGGTTCATTGTATAAGTATCCTCCCTTGATTGGTCGAATATTAGGCATGCCCCGGGAGCATGTGGGCTCGAGCCACGGAGAGCAACTAATCGCGCATAAAACAAATACCTCATGGTTTTTGTGCGGAAAACCGTTGGGTGGACCATCAGCGGTTGTGATT</span>
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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="LC9" class="line" lang="plaintext">>bkpt1<span class="idiff left deletion">6</span>_Seq3_pos_781_fuzzy_0_HOM_len_111_qual_50_avg_cov_<span class="idiff deletion">2</span>0.<span class="idiff deletion">8</span>5_median_cov_<span class="idiff right deletion">20.5</span>0 </span>
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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">>bkpt1<span class="idiff left addition">4</span>_Seq3_pos_781_fuzzy_0_HOM_len_111_qual_50_avg_cov_<span class="idiff addition">5</span>0.5<span class="idiff addition">4</span>_median_cov_<span class="idiff right addition">53.0</span>0 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">TTTGCAGCACTAGCCGTTCCTTGACATCTGCGGCCAACTTGTGCCTGAACCTGGAGTTTCGACAGCGTGGCGCTCTGGCCTAGTTCTTCGCTGGCACCTGGAAGAGCCGCC</span>
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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="LC11" class="line" lang="plaintext">>bkpt1<span class="idiff left deletion">8</span>_Seq4_pos_351_fuzzy_2_HET_len_120_qual_50_avg_cov_<span class="idiff deletion">9.73</span>_median_cov_<span class="idiff right deletion">10</span>.00 </span>
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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="LC11" class="line" lang="plaintext">>bkpt1<span class="idiff left addition">6</span>_Seq4_pos_351_fuzzy_2_HET_len_120_qual_50_avg_cov_<span class="idiff addition">25.67</span>_median_cov_<span class="idiff right addition">26</span>.00 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">GTCTTAACCTTAAGACCGTTCATTGATAAAACTTGCTCACGCTCTAGATGGCGTGAAGCGAAACCTAGGAAAAAGTTTTGCAGATAATTAGATTATGCGCGATACTCCGCCGTGTGTTCA</span>
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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="LC13" class="line" lang="plaintext">>bkpt<span class="idiff left deletion">20</span>_Seq4_pos_603_fuzzy_3_HOM_len_57_qual_50_avg_cov_<span class="idiff deletion">22.71</span>_median_cov_<span class="idiff right deletion">23</span>.00 </span>
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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="LC13" class="line" lang="plaintext">>bkpt<span class="idiff left addition">18</span>_Seq4_pos_603_fuzzy_3_HOM_len_57_qual_50_avg_cov_<span class="idiff addition">46.66</span>_median_cov_<span class="idiff right addition">47</span>.00 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">TGTATTCCTGGGTTGAGTGGCAGGTTTCTCTTAATTCTTCCCTAAGTAGCTCCGAGG</span>
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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="LC15" class="line" lang="plaintext">>bkpt2<span class="idiff left deletion">2</span>_Seq4_pos_821_fuzzy_0_HOM_len_40_qual_50_avg_cov_<span class="idiff deletion">24.34</span>_median_cov_<span class="idiff right deletion">24</span>.00 </span>
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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="LC15" class="line" lang="plaintext">>bkpt2<span class="idiff left addition">0</span>_Seq4_pos_821_fuzzy_0_HOM_len_40_qual_50_avg_cov_<span class="idiff addition">37.63</span>_median_cov_<span class="idiff right addition">38</span>.00 </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">GGATGGCGGCCGGAGAGCGCTGCAATCGCATGGCTCGGGA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#c8c1994bf5a622886714f298cf13c1bdff72d28c"><strong>test/full_test/gold.insertions.vcf</strong></a>
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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="plaintext">##fileformat=VCFv4.1</span>
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left deletion">hu May</span> <span class="idiff deletion">9</span> 1<span class="idiff deletion">1:36:09</span> 20<span class="idiff right deletion">19</span></span>
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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="LC3" class="line" lang="plaintext">##source=MindTheGap fill version 2.2.<span class="idiff left right deletion">0</span></span>
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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="plaintext">##SAMPLE=file:<span class="idiff left right deletion">test-output/full-test</span>.h5</span>
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5
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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="LC5" class="line" lang="plaintext">##REF=file:<span class="idiff left right deletion">test-output/full-test</span></span>
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2
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left addition">ue Feb</span> <span class="idiff addition">8</span> 1<span class="idiff addition">2:29:50</span> 20<span class="idiff right addition">22</span></span>
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3
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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="LC3" class="line" lang="plaintext">##source=MindTheGap fill version 2.2.<span class="idiff left right addition">3</span></span>
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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="LC4" class="line" lang="plaintext">##SAMPLE=file:<span class="idiff left right addition">gold</span>.h5</span>
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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="LC5" class="line" lang="plaintext">##REF=file:<span class="idiff left right addition">gold</span></span>
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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">##INFO=<ID=TYPE,Number=1,Type=String,Description="INS"></span>
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7
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">##INFO=<ID=LEN,Number=1,Type=Integer,Description="variant size"></span>
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8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">##INFO=<=QUAL,Number=.,Type=Integer,Description="Quality of the insertion"></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">@@ -12,11 +12,11 @@</td>
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12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">##INFO=<ID=NPOS,Number=1,Type=Integer,Description="number of alternative positions for the insertion site (= size of repeat (fuzzy) +1)"></span>
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13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1</span>
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15
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC15" class="line" lang="plaintext">Seq0 123 bkpt2 G GATCTAAGCTGTGACCTTGTGGCCGAGGCGCTTTTCACGCCTACATTAACTCCTGGGAAGCTCTCTGCTCTAGTTTCAGTGCACATCTCCAGGTGAGCAACCCTGGCAAGCAGCCCCTTCCTGTAGAAATTACTTAGC . PASS TYPE=INS;LEN=137;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff left deletion">8.38</span>;MDK=<span class="idiff right deletion">8</span>.00 GT 0/1</span>
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16
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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="LC16" class="line" lang="plaintext">Seq1 342 bkpt<span class="idiff left deletion">6</span> T TATGGTTTATAGAACCCGGGCGTTCATGTCCGTCAGAACGATCTTGGCACGGTAGCCCCTGGTCCAGAGAGCCAAGGTGACTCAGCCCCACGATGGTGGTCTAGAGCGAAATAACCCTCGCCGAGA . PASS TYPE=INS;LEN=125;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff deletion">9.91</span>;MDK=<span class="idiff right deletion">9</span>.00 GT 0/1</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC17" class="line" lang="plaintext">Seq2 535 bkpt<span class="idiff left deletion">11</span> G GTAACGTTCGCTGAACATCGACTCCGGTGACGACATACGATTCAAGAAGAGAGTGACTCTGTAGGATAACATCCCGCAACGCCTAATCCATCCAGCCTGGCACCATGTATAAAGGGCGTCAGGTATGTTAACGAGACTATT . PASS TYPE=INS;LEN=140;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff deletion">2</span>1.6<span class="idiff deletion">3</span>;MDK=<span class="idiff right deletion">22</span>.00 GT 1/1</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC18" class="line" lang="plaintext">Seq2 834 bkpt1<span class="idiff left deletion">2</span> A ATGCACGCTGCAGGATTGGAACCACAATGTACGCCGATCCAAGCAGTAGTGGTTCATTGTATAAGTATCCTCCCTTGATTGGTCGAATATTAGGCATGCCCCGGGAGCATGTGGGCTCGAGCCACGGAGAGCAACTAATCGCGCATAAAACAAATACCTCATGGTTTTTGTGCGGAAAACCGTTGGGTGGACCATCAGCGGTTGTGAT . PASS TYPE=INS;LEN=207;QUAL=50;NSOL=1;NPOS=2;AVK=<span class="idiff deletion">16.50</span>;MDK=<span class="idiff right deletion">16</span>.00 GT 1/1</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC19" class="line" lang="plaintext">Seq3 781 bkpt1<span class="idiff left deletion">6</span> G GTTTGCAGCACTAGCCGTTCCTTGACATCTGCGGCCAACTTGTGCCTGAACCTGGAGTTTCGACAGCGTGGCGCTCTGGCCTAGTTCTTCGCTGGCACCTGGAAGAGCCGCC . PASS TYPE=INS;LEN=111;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff deletion">2</span>0.<span class="idiff deletion">8</span>5;MDK=<span class="idiff right deletion">20.5</span>0 GT 1/1</span>
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20
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC20" class="line" lang="plaintext">Seq4 349 bkpt1<span class="idiff left deletion">8</span> G GCAGTCTTAACCTTAAGACCGTTCATTGATAAAACTTGCTCACGCTCTAGATGGCGTGAAGCGAAACCTAGGAAAAAGTTTTGCAGATAATTAGATTATGCGCGATACTCCGCCGTGTGTT . PASS TYPE=INS;LEN=120;QUAL=50;NSOL=1;NPOS=3;AVK=<span class="idiff deletion">9.73</span>;MDK=<span class="idiff right deletion">10</span>.00 GT 0/1</span>
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21
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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="LC21" class="line" lang="plaintext">Seq4 600 bkpt<span class="idiff left deletion">20</span> T TAGGTGTATTCCTGGGTTGAGTGGCAGGTTTCTCTTAATTCTTCCCTAAGTAGCTCCG . PASS TYPE=INS;LEN=57;QUAL=50;NSOL=1;NPOS=4;AVK=<span class="idiff deletion">22.71</span>;MDK=<span class="idiff right deletion">23</span>.00 GT 1/1</span>
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22
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC22" class="line" lang="plaintext">Seq4 821 bkpt2<span class="idiff left deletion">2</span> C CGGATGGCGGCCGGAGAGCGCTGCAATCGCATGGCTCGGGA . PASS TYPE=INS;LEN=40;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff deletion">24.34</span>;MDK=<span class="idiff right deletion">24</span>.00 GT 1/1</span></pre></td>
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15
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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="LC15" class="line" lang="plaintext">Seq0 123 bkpt2 G GATCTAAGCTGTGACCTTGTGGCCGAGGCGCTTTTCACGCCTACATTAACTCCTGGGAAGCTCTCTGCTCTAGTTTCAGTGCACATCTCCAGGTGAGCAACCCTGGCAAGCAGCCCCTTCCTGTAGAAATTACTTAGC . PASS TYPE=INS;LEN=137;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff left addition">21.59</span>;MDK=<span class="idiff right addition">21</span>.00 GT 0/1</span>
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16
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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="LC16" class="line" lang="plaintext">Seq1 342 bkpt<span class="idiff left addition">5</span> T TATGGTTTATAGAACCCGGGCGTTCATGTCCGTCAGAACGATCTTGGCACGGTAGCCCCTGGTCCAGAGAGCCAAGGTGACTCAGCCCCACGATGGTGGTCTAGAGCGAAATAACCCTCGCCGAGA . PASS TYPE=INS;LEN=125;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff addition">25.17</span>;MDK=<span class="idiff right addition">24</span>.00 GT 0/1</span>
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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="LC17" class="line" lang="plaintext">Seq2 535 bkpt<span class="idiff left addition">9</span> G GTAACGTTCGCTGAACATCGACTCCGGTGACGACATACGATTCAAGAAGAGAGTGACTCTGTAGGATAACATCCCGCAACGCCTAATCCATCCAGCCTGGCACCATGTATAAAGGGCGTCAGGTATGTTAACGAGACTATT . PASS TYPE=INS;LEN=140;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff addition">4</span>1.6<span class="idiff addition">6</span>;MDK=<span class="idiff right addition">43</span>.00 GT 1/1</span>
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18
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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="LC18" class="line" lang="plaintext">Seq2 834 bkpt1<span class="idiff left addition">0</span> A ATGCACGCTGCAGGATTGGAACCACAATGTACGCCGATCCAAGCAGTAGTGGTTCATTGTATAAGTATCCTCCCTTGATTGGTCGAATATTAGGCATGCCCCGGGAGCATGTGGGCTCGAGCCACGGAGAGCAACTAATCGCGCATAAAACAAATACCTCATGGTTTTTGTGCGGAAAACCGTTGGGTGGACCATCAGCGGTTGTGAT . PASS TYPE=INS;LEN=207;QUAL=50;NSOL=1;NPOS=2;AVK=<span class="idiff addition">40.42</span>;MDK=<span class="idiff right addition">42</span>.00 GT 1/1</span>
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19
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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="LC19" class="line" lang="plaintext">Seq3 781 bkpt1<span class="idiff left addition">4</span> G GTTTGCAGCACTAGCCGTTCCTTGACATCTGCGGCCAACTTGTGCCTGAACCTGGAGTTTCGACAGCGTGGCGCTCTGGCCTAGTTCTTCGCTGGCACCTGGAAGAGCCGCC . PASS TYPE=INS;LEN=111;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff addition">5</span>0.5<span class="idiff addition">4</span>;MDK=<span class="idiff right addition">53.0</span>0 GT 1/1</span>
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20
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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="LC20" class="line" lang="plaintext">Seq4 349 bkpt1<span class="idiff left addition">6</span> G GCAGTCTTAACCTTAAGACCGTTCATTGATAAAACTTGCTCACGCTCTAGATGGCGTGAAGCGAAACCTAGGAAAAAGTTTTGCAGATAATTAGATTATGCGCGATACTCCGCCGTGTGTT . PASS TYPE=INS;LEN=120;QUAL=50;NSOL=1;NPOS=3;AVK=<span class="idiff addition">25.67</span>;MDK=<span class="idiff right addition">26</span>.00 GT 0/1</span>
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21
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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="LC21" class="line" lang="plaintext">Seq4 600 bkpt<span class="idiff left addition">18</span> T TAGGTGTATTCCTGGGTTGAGTGGCAGGTTTCTCTTAATTCTTCCCTAAGTAGCTCCG . PASS TYPE=INS;LEN=57;QUAL=50;NSOL=1;NPOS=4;AVK=<span class="idiff addition">46.66</span>;MDK=<span class="idiff right addition">47</span>.00 GT 1/1</span>
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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="LC22" class="line" lang="plaintext">Seq4 821 bkpt2<span class="idiff left addition">0</span> C CGGATGGCGGCCGGAGAGCGCTGCAATCGCATGGCTCGGGA . PASS TYPE=INS;LEN=40;QUAL=50;NSOL=1;NPOS=1;AVK=<span class="idiff addition">37.63</span>;MDK=<span class="idiff right addition">38</span>.00 GT 1/1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#b10c092b7d0dc2e98cf5cacfce65a2504da2ab6c"><strong>test/full_test/gold.othervariants.vcf</strong></a>
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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="plaintext">##fileformat=VCFv4.1</span>
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left deletion">hu May</span> <span class="idiff deletion">9</span> 1<span class="idiff deletion">1:49:49</span> 20<span class="idiff right deletion">19</span></span>
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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="LC3" class="line" lang="plaintext">##source=MindTheGap find version 2.2.<span class="idiff left right deletion">0</span></span>
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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="plaintext">##SAMPLE=file:../data/reads_r1.fastq,../data/reads_r2.fastq</span>
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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="LC5" class="line" lang="plaintext">##REF=file:../data/reference.fasta</span>
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left addition">ue Feb</span> <span class="idiff addition">8</span> 1<span class="idiff addition">2:29:50</span> 20<span class="idiff right addition">22</span></span>
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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="LC3" class="line" lang="plaintext">##source=MindTheGap find version 2.2.<span class="idiff left right addition">3</span></span>
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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="LC4" class="line" lang="plaintext">##SAMPLE=file:../<span class="idiff left addition">../</span>data/reads_r1.fastq,../<span class="idiff right addition">../</span>data/reads_r2.fastq</span>
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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="LC5" class="line" lang="plaintext">##REF=file:../<span class="idiff left right addition">../</span>data/reference.fasta</span>
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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">##INFO=<ID=TYPE,Number=1,Type=String,Description="SNP, INS, DEL or ."></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">##INFO=<ID=LEN,Number=1,Type=Integer,Description="variant size"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">##INFO=<ID=FUZZY,Number=1,Type=Integer,Description="repeat size at the breakpoint, only for INS and DEL"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1</span>
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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">Seq0 101 bkpt1 T C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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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="LC12" class="line" lang="plaintext">Seq0 816 bkpt3 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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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="LC13" class="line" lang="plaintext">Seq1 206 bkpt4 G C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Seq1 219 bkpt5 T A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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15
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Seq1 740 bkpt7 CCTGTTGGGAAGGAATTGCAATACTCTCCGAACCAGCTTAGGGCCCCCCGCCGCCGCAATTCGAGCGTTATGCCCGGAGCATTTGCACGATGCCATTAAACTATATCAA C . PASS TYPE=DEL;LEN=108;FUZZY=2 GT 1/1</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Seq2 320 bkpt8 T C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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17
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Seq2 344 bkpt9 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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18
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Seq2 379 bkpt10 G C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Seq3 256 bkpt13 A T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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20
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Seq3 511 bkpt14 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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21
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Seq3 766 bkpt15 G A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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22
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Seq4 257 bkpt17 C T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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23
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Seq4 512 bkpt19 A G . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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24
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Seq4 841 bkpt21 C T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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25
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Seq4 884 bkpt23 CTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGG C . PASS TYPE=DEL;LEN=44;FUZZY=2 GT 1/1</span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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12
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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="LC12" class="line" lang="plaintext">Seq0 297 bkpt3 CTAGCTTGAGAGTGCGTATCTCACCGATCCCCTGGCTATGCTCCGCGATTCACTAGTAGTTTCACGCCGACAGAGCGAAACCGTGATAGGTCATCATGCCGGTCTGCAGTCACGT C . PASS TYPE=DEL;LEN=114;FUZZY=0 GT 1/1</span>
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13
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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="LC13" class="line" lang="plaintext">Seq0 816 bkpt4 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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14
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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="LC14" class="line" lang="plaintext">Seq2 320 bkpt6 T C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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15
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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="LC15" class="line" lang="plaintext">Seq2 344 bkpt7 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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16
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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="LC16" class="line" lang="plaintext">Seq2 379 bkpt8 G C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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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="LC17" class="line" lang="plaintext">Seq3 256 bkpt11 A T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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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="LC18" class="line" lang="plaintext">Seq3 511 bkpt12 C A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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19
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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="LC19" class="line" lang="plaintext">Seq3 766 bkpt13 G A . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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20
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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="LC20" class="line" lang="plaintext">Seq4 257 bkpt15 C T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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21
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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="LC21" class="line" lang="plaintext">Seq4 512 bkpt17 A G . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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22
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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="LC22" class="line" lang="plaintext">Seq4 841 bkpt19 C T . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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23
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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="LC23" class="line" lang="plaintext">Seq4 884 bkpt21 CTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGG C . PASS TYPE=DEL;LEN=44;FUZZY=2 GT 1/1</span>
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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="LC24" class="line" lang="plaintext">Seq5 100 bkpt22 T TC . PASS TYPE=INS;LEN=1;FUZZY=1 GT 1/1</span>
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27
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28
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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="LC28" class="line" lang="plaintext">Seq5 500 bkpt26 C CT . PASS TYPE=INS;LEN=1;FUZZY=0 GT 1/1</span>
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29
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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="LC29" class="line" lang="plaintext">Seq5 600 bkpt27 G GA . PASS TYPE=INS;LEN=1;FUZZY=0 GT 0/1</span>
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30
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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="LC30" class="line" lang="plaintext">Seq5 700 bkpt28 A AC . PASS TYPE=INS;LEN=1;FUZZY=0 GT 0/1</span>
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31
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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="LC31" class="line" lang="plaintext">Seq5 800 bkpt29 A AC . PASS TYPE=INS;LEN=1;FUZZY=2 GT 0/1</span>
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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="LC32" class="line" lang="plaintext">Seq5 900 bkpt30 T TG . PASS TYPE=INS;LEN=1;FUZZY=2 GT 0/1</span>
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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="LC33" class="line" lang="plaintext">Seq6 98 bkpt31 T TAT . PASS TYPE=INS;LEN=2;FUZZY=3 GT 1/1</span>
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34
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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="LC34" class="line" lang="plaintext">Seq6 200 bkpt32 A ACG . PASS TYPE=INS;LEN=2;FUZZY=1 GT 1/1</span>
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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="LC35" class="line" lang="plaintext">Seq6 300 bkpt33 A ATA . PASS TYPE=INS;LEN=2;FUZZY=1 GT 1/1</span>
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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="LC36" class="line" lang="plaintext">Seq6 400 bkpt34 T TCA . PASS TYPE=INS;LEN=2;FUZZY=0 GT 1/1</span>
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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="LC37" class="line" lang="plaintext">Seq6 600 bkpt35 T TCA . PASS TYPE=INS;LEN=2;FUZZY=0 GT 0/1</span>
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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="LC38" class="line" lang="plaintext">Seq6 699 bkpt36 C CGT . PASS TYPE=INS;LEN=2;FUZZY=2 GT 0/1</span>
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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="LC39" class="line" lang="plaintext">Seq6 800 bkpt37 T TGG . PASS TYPE=INS;LEN=2;FUZZY=0 GT 0/1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#67a55931ce6762bb201dd046914354503475d9c4"><strong>test/full_test/gold_bed.breakpoints</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,11 +2,11 @@</td>
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2
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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="plaintext">CTCCGGATCTCCGTGTTCTTCGGAAGCTTAG</span>
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3
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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="plaintext">>bkpt2_Seq0_pos_123_fuzzy_0_HET right_kmer</span>
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4
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">GTCACGCGCGTCATACTACAGTAAGTTACTG</span>
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5
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">3</span>_Seq1_pos_342_fuzzy_0_HET left_kmer</span>
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5
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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="LC5" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">4</span>_Seq1_pos_342_fuzzy_0_HET left_kmer</span>
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6
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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">GCCGCGCAAAGCCGGTCAACAGCGTTAGTAT</span>
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7
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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="LC7" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">3</span>_Seq1_pos_342_fuzzy_0_HET right_kmer</span>
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">GTTGAAAGTTTACTCAGATCGCTTCTGTCGG</span>
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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="LC9" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">4</span>_Seq2_pos_535_fuzzy_0_HOM left_kmer</span>
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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">>bkpt<span class="idiff left right addition">5</span>_Seq2_pos_535_fuzzy_0_HOM left_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">GGCATGCGTAAGTTATCGTGAAACCATGATG</span>
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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="LC11" class="line" lang="plaintext">>bkpt<span class="idiff left right deletion">4</span>_Seq2_pos_535_fuzzy_0_HOM right_kmer</span>
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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="LC11" class="line" lang="plaintext">>bkpt<span class="idiff left right addition">5</span>_Seq2_pos_535_fuzzy_0_HOM right_kmer</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">GCCCCTTACTAGACCAAATGTACTGAATGCG</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#4080c9c6d095c9d4cdfe76f895c2390e2965c90c"><strong>test/full_test/gold_bed.othervariants.vcf</strong></a>
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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="plaintext">##fileformat=VCFv4.1</span>
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left deletion">hu May</span> <span class="idiff deletion">9</span> 1<span class="idiff deletion">1</span>:4<span class="idiff deletion">0:18</span> 20<span class="idiff right deletion">19</span></span>
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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="LC3" class="line" lang="plaintext">##source=MindTheGap find version 2.2.<span class="idiff left right deletion">0</span></span>
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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="LC2" class="line" lang="plaintext">##filedate=T<span class="idiff left addition">ue Feb</span> <span class="idiff addition">8</span> 1<span class="idiff addition">2</span>:4<span class="idiff addition">6:04</span> 20<span class="idiff right addition">22</span></span>
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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="LC3" class="line" lang="plaintext">##source=MindTheGap find version 2.2.<span class="idiff left right addition">3</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">##SAMPLE=file:../../data/reads_r1.fastq,../../data/reads_r2.fastq</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">##REF=file:../../data/reference.fasta</span>
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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">##INFO=<ID=TYPE,Number=1,Type=String,Description="SNP, INS, DEL or ."></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">@@ -9,3 +9,4 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1</span>
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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">Seq0 101 bkpt1 T C . PASS TYPE=SNP;LEN=1;FUZZY=0 GT 1/1</span>
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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="LC12" class="line" lang="plaintext">Seq0 297 bkpt3 CTAGCTTGAGAGTGCGTATCTCACCGATCCCCTGGCTATGCTCCGCGATTCACTAGTAGTTTCACGCCGACAGAGCGAAACCGTGATAGGTCATCATGCCGGTCTGCAGTCACGT C . PASS TYPE=DEL;LEN=114;FUZZY=0 GT 1/1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#7b53f04776f31332bc381ffecb609a18ba6a21e2"><strong>test/full_test/gold_fill.output</strong></a>
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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="plaintext">MindTheGap fill </span>
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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="LC3" class="line" lang="plaintext"> version : <span class="idiff left right deletion">1.0.0</span></span>
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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="plaintext"> gatb-core-library : 1.<span class="idiff left right deletion">2.0</span></span>
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2
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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="LC2" class="line" lang="plaintext"> version : <span class="idiff left right addition">2.2.3</span></span>
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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="LC3" class="line" lang="plaintext"> gatb-core-library : 1.<span class="idiff left right addition">4.2</span></span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> supported_kmer_sizes : 32 64 96 128</span>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Parameters </span>
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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"> Input data </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">@@ -9,18 +8,21 @@ Parameters</td>
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9
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Breakpoints : gold.breakpoints</span>
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10
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Graph </span>
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11
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> kmer-size : 31</span>
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12
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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="LC12" class="line" lang="plaintext"> abundance_min (auto inferred) : <span class="idiff left right deletion">3</span> </span>
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13
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> abundance_min (used) : <span class="idiff left right deletion">3</span></span>
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14
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> nb_solid_kmers : <span class="idiff left right deletion">5473</span></span>
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15
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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="LC15" class="line" lang="plaintext"> nb_branching_nodes : 3<span class="idiff left right deletion">4</span></span>
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11
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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="LC11" class="line" lang="plaintext"> abundance_min (auto inferred) : <span class="idiff left right addition">7</span> </span>
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12
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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="LC12" class="line" lang="plaintext"> abundance_min (used) : <span class="idiff left right addition">7</span></span>
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13
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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="LC13" class="line" lang="plaintext"> nb_solid_kmers : <span class="idiff left right addition">7419</span></span>
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14
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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="LC14" class="line" lang="plaintext"> nb_branching_nodes : 3<span class="idiff left right addition">6</span></span>
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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> Assembly options </span>
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17
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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> max_depth : 10000</span>
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18
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17
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> max_nodes : 100</span>
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19
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18
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Results </span>
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20
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19
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> Breakpoints </span>
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21
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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="LC21" class="line" lang="plaintext"> nb_input : 7</span>
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22
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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="LC22" class="line" lang="plaintext"> nb_filled : 7</span>
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23
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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="LC23" class="line" lang="plaintext"> unique_sequence : 7</span>
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24
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25
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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="LC25" class="line" lang="plaintext"> Time : 0.0 s</span>
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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="LC26" class="line" lang="plaintext"> Output file : gold.insertions.fasta</span></pre></td>
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20
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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="LC20" class="line" lang="plaintext"> nb_input_breakpoints : 8</span>
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21
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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="LC21" class="line" lang="plaintext"> nb_filled_breakpoints : 8</span>
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22
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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="LC22" class="line" lang="plaintext"> as_unique_sequence : 8</span>
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23
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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="LC23" class="line" lang="plaintext"> as_multiple_sequence : 0</span>
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24
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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="LC24" class="line" lang="plaintext"> Time : 1.0 s</span>
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25
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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="LC25" class="line" lang="plaintext"> Output files </span>
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26
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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="LC26" class="line" lang="plaintext"> assembled sequence file : gold.insertions.fasta</span>
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27
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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="LC27" class="line" lang="plaintext"> insertion variant vcf file : gold.insertions.vcf</span>
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28
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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="LC28" class="line" lang="plaintext"> assembly statistics file : gold.info.txt</span></pre></td>
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<li id="c16df07c21fdc174b1138d12fda1474cca58c93c">
<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#c16df07c21fdc174b1138d12fda1474cca58c93c"><strong>test/full_test/gold_find.output</strong></a>
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1
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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="plaintext">MindTheGap find </span>
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2
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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2" class="line" lang="plaintext"> version : <span class="idiff left right deletion">1.0.0</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3" class="line" lang="plaintext"> gatb-core-library : 1.<span class="idiff left right deletion">2.0</span></span>
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2
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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="LC2" class="line" lang="plaintext"> version : <span class="idiff left right addition">2.2.3</span></span>
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3
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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="LC3" class="line" lang="plaintext"> gatb-core-library : 1.<span class="idiff left right addition">4.2</span></span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> supported_kmer_sizes : 32 64 96 128</span>
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Parameters </span>
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6
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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"> Input data </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">@@ -8,11 +8,11 @@ Parameters</td>
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Reference : ../../data/reference.fasta</span>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Graph </span>
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> kmer-size : 31</span>
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11
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> abundance_min (auto inferred) : <span class="idiff left right deletion">3</span> </span>
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12
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> abundance_min (used) : <span class="idiff left right deletion">3</span></span>
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11
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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="LC11" class="line" lang="plaintext"> abundance_min (auto inferred) : <span class="idiff left right addition">7</span> </span>
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12
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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="LC12" class="line" lang="plaintext"> abundance_min (used) : <span class="idiff left right addition">7</span></span>
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13
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13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> abundance_max : 2147483647</span>
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14
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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="LC14" class="line" lang="plaintext"> nb_solid_kmers : <span class="idiff left right deletion">5473</span></span>
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15
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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="LC15" class="line" lang="plaintext"> nb_branching_nodes : 3<span class="idiff left right deletion">4</span></span>
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14
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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="LC14" class="line" lang="plaintext"> nb_solid_kmers : <span class="idiff left right addition">7419</span></span>
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15
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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="LC15" class="line" lang="plaintext"> nb_branching_nodes : 3<span class="idiff left right addition">6</span></span>
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16
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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Breakpoint detection options </span>
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17
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17
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> max_repeat : 5</span>
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18
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18
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> hetero_max_occ : 1</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">@@ -25,12 +25,14 @@ Results</td>
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25
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25
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> homozygous : 5</span>
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26
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26
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> clean : 3</span>
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27
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27
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> fuzzy : 2</span>
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28
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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="LC28" class="line" lang="plaintext"> heterozygous : <span class="idiff left right deletion">2</span></span>
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29
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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="LC29" class="line" lang="plaintext"> clean : <span class="idiff left right deletion">1</span></span>
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28
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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="LC28" class="line" lang="plaintext"> heterozygous : <span class="idiff left right addition">3</span></span>
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29
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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="LC29" class="line" lang="plaintext"> clean : <span class="idiff left right addition">2</span></span>
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30
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30
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> fuzzy : 1</span>
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31
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31
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> Other variants </span>
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32
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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="LC32" class="line" lang="plaintext"> deletions : 3</span>
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33
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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="LC33" class="line" lang="plaintext"> SNPs : 13</span>
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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="LC32" class="line" lang="plaintext"> deletions : 2</span>
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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="LC33" class="line" lang="plaintext"> Homozygous insertions 1-2 bp size : 9</span>
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34
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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="LC34" class="line" lang="plaintext"> Heterozygous insertions 1-2 bp size : 7</span>
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35
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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="LC35" class="line" lang="plaintext"> SNPs : 11</span>
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34
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36
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> Time : 0.0 s</span>
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35
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37
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> Output files </span>
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36
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38
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> graph_file : gold.h5</span>
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<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b905744345c06c4c96602510025ab2bf5aefebbc#0a923f8b74d7d5281f2efcf05d27306273c4e75f"><strong>test/full_test/reference.fasta</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">@@ -8,3 +8,7 @@ TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCG</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTAATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGCTGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAGGTATCCTTACTTTCGGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC</span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">>Seq4</span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACCCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAAGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCCCGAACATTGAGACCTGGCCAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGGTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT</span>
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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="LC11" class="line" lang="plaintext">>Seq5</span>
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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="LC12" class="line" lang="plaintext">GATGTTTAGAAGTTTCCAGGTCACGCCAATGATTGGCATTTACACACGTGGATCAGCGGACATATCTAACCCTTAGTGTTCTTAAGAGCAACTCACTACTCATTTCCACTAACCCCGCCGGCGGTAATTCCAATCTAGTTGATCAGACTTCCCAGTCAATGAAAGCGACACCGTGCGTCTGTAATACCAACAAGACCCTGCTGTCGTCCCGCAGAGGACGCGGCACCTCCGGATTTTGAGTCCAGTCTGAACGATTTTCGATCACTCACCATGGATCTGGAAAACGGAGTCGAGTACTCAGAGCCAAATTGATGCATTTCCAATGACCCGATGCAGGTGCGACCGATCTTCGCCTATGCTTCCCGCCGTAATTATTGAGTCTGGGTCCCGGCCGCTAACGTTGACTCACGGGGAGGTACCCGTGCGTATTCTTCTCAAAGTGACGCTGGACAGCAGCGCATGTCCGAGCCCCATCGTCCTATCTGGTGTAGAGTCTTACCCTAATTAGAGTGATCGAACCAGTAGGTGTCGCGGTCTTAGGGCTCCCATTGTCCAAGGGAACGTGAACAGATATGAATCTGGGAGAATAGTGCAGCGTTGCCCTTCTGGTCGGTCAGCCCTTGCCTACGGCCCGTATGCGGAGAATGAAGGCGTGAAACATTCTGCTCTTTTAGAAGCAGCGGCTGCACCCGTATAACAATCGCACGATCGTACGTCTCATTTGCCGCGTTGGCGCGCCCGTGGATGATGGACCACGGTATGAACCTCTGCACTTCAAATTTGACGCAATCCTGCACTCACCGCACACAGTTCTAGTCTAACCGTCGCAGTGTCTGCTTTAAGGTAGAGATCGATACTTAGGATATGTTCATGTGTGTTTGTAGCGCTGGACCCTCTTATGGTGTGGTCACTTGTGATGGATCGAGGAACTTAGGCGGTTAACTTGTTTCGACGTCTCACCGACAATATCAGGATTTAGTATCG</span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">>Seq6</span>
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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="LC14" class="line" lang="plaintext">ACCGAAAATGACAATGTTCACACGCATGCTCGGCGTGGAAAAGAGCCTTTTCTAAGACCGACTCGTTCCGGGCAGCAGGATTATTAGCCAATCAAAATTATCGACCGGTCATCAAGCTGCGATAGTGCAGGCGCATGCCGTCCAATGGGTCCACGGCGGAAGTGCGTTCGTCTACTCTGTCAAATCTTAACATTTTTTGAGGCTAATCCGGCCGGTAGTGTACCGTGAACCAAAGTCCTTCTACGAGCGTATTAGATTGCTCAAAAGATCCGGGAGAATTGACCAGGTCGTATCTTTAAAAACGCTGGTGCGAGCAGCTGCTGTTTTATCAACACCCATTTAGTCCTGTGAAGTTTGCTTAGCAGATACACCTTCCCGCGTGGTATGAGAGGCTGTTCTTTTAAAAACTATGAGGCTCTGGCACCTTCGACGCTAACAAAGTCCCCACGGACCATGATACCCTTACGCAACTCTCTTTGCACGCTAGGGCGAGAGTACTGCCCCTAGACTAGGTACACGCCGGGTAAACTCTCTCGCACACCTTTACGCTCGACTACAGGCTTCTAACCCTTCCGAACGCATATAATTCAAATGGCACTTAGTAACAGACGAATCACGGCTCACAGGCAGAATTCACTGGAGTAAAAGGATTCAGAACAATAGATAGTGTGTTAACTTTACAGTCATCCGTATTATAACGTAGCGAGAGGATTGAGTTCTTGTTAGGAAGGAAGGTCCTATAGACGAGTGCGGTAGCGCACCCGGTCGCCTTGCGTAGTCATGCCCGACGTGTTGATGGTTCCCTTTTAGCCGCCACACAAGGGATCCGAGGGTGAGAGACACATGGCCCTCACCGACGAGACTTACTCAGCCTGCCTCGCTATTGCCCTCTTTTTGATCGTCCCTTTGTGGCTCTCGAGGACTCGTGCAGCGTGTATCTGGGGATTTGTAAGCTTAAGACTACCTTCCATAGGA</span></pre></td>
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