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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/b7bdcbee246d474229b51a2960c60e0f6caaf96c">b7bdcbee</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-09-21T21:08:16+05:30</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.3</pre>

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<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

CHANGELOG.md

</a>

</li>

<li class="file-stats">

<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">

CMakeLists.txt

</a>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#1dd61bb768b613b358467981e3d64ec6394b090d">

doc/MindTheGap_insertion_caller.md

</a>

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<li class="file-stats">

<a href="#adece0878a8a457c3376d5aaf5b9a31d65f26181">

src/Filler.cpp

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<li class="file-stats">

<a href="#7dee9a67d61921d9c899a1345a2272b965b1fde4">

src/Filler.hpp

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<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">

src/main.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Unreleased]</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> 2 novel options in the <span class="sb" style="color: #d14;">`Fill`</span> (local assembly) module :</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">  *</span> <span class="sb" style="color: #d14;">`-fwd-only`</span>:  output the first-contig extensions of failed gap-fillings in a separate file, it can be useful for the assembly of the extremities of linear genomes (as in the <span class="p">[</span><span class="nv" style="color: #008080;">MinYS</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/cguyomar/MinYS</span><span class="p">)</span> tool)</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">  *</span> <span class="sb" style="color: #d14;">`-extend`</span>:  do not try in reverse direction if no inserted sequence is assembled (bkpt mode), it can improve the running time and/or help the user controlling the direction of assembly (as in the <span class="p">[</span><span class="nv" style="color: #008080;">MTG-link</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/anne-gcd/MTG-Link</span><span class="p">)</span> tool)</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">--------------------------------------------------------------------------------</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [2.2.2] - 2020-06-19</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">*</span> A bug fix: updating gatb-core version, notably this fixes a bug in the <span class="sb" style="color: #d14;">`fill`</span> module: nodes at extremities of contigs of size exactly <span class="sb" style="color: #d14;">`k`</span> were not marked correctly, potentially leading to duplicated contigs in the contig graph. This could prevent exploring some parts of the graph, and if graph exploration parameters where set too large (<span class="sb" style="color: #d14;">`-max-nodes`</span> and <span class="sb" style="color: #d14;">`-max-length`</span>), it could lead in some rare cases to extreme running times and/or memory consumptions. This should no longer happen now.</span>

</pre>

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<br>

</li>

<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>

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<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>

</pre>

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<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>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR 2<span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); 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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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">2</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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">3</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); 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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cmake"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); 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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="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>

</pre>

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="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>

</pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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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">@@ -4,9 +4,9 @@</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">|-----------|-------------|</span>

</pre>

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

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

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<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>

</pre>

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

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

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); 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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="idiff left">Travis CI : </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![Build Status</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://travis-ci.org/GATB/MindTheGap.svg?branch=master</span></span><span class="p">)</span>](http<span class="idiff">s</span>://<span class="idiff">travis-ci.org/GATB/M</span>ind<span class="idiff">T</span>he<span class="idiff right">G</span>ap)</span>

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![install with bioconda</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span></span><span class="p">)</span>](http://<span class="idiff">bioconda.github.io/recipes/m</span>ind<span class="idiff">t</span>he<span class="idiff">g</span>ap<span class="idiff right">/README.html</span>)</span>

</pre>

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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">

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<td class="new_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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); 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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License</span><span class="p">](</span><span class="sx" style="color: #d14;">http://img.shields.io/:license-affero-blue.svg</span><span class="p">)</span>](http://www.gnu.org/licenses/agpl-3.0.en.html)</span>

</pre>

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

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

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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"><span class="p">[</span><span class="nv" style="color: #008080;">![License</span><span class="p">](</span><span class="sx" style="color: #d14;">http://img.shields.io/:license-affero-blue.svg</span><span class="p">)</span>](http://www.gnu.org/licenses/agpl-3.0.en.html)<span class="idiff left right">     </span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># What is MindTheGap ?</span></span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,10 +49,7 @@ Retrieve a binary archive file from one of the official MindTheGap releases (see</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="sb" style="color: #d14;">    tar -zxf MindTheGap-vX.Y.Z-bin-Darwin.tar.gz</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;">    cd MindTheGap-vX.Y.Z-bin-Darwin</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;">    chmod u+x bin/MindTheGap</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;">    # run a simple example</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ./bin/MindTheGap find -in data/reads_r1.fastq,data/reads_r2.fastq -ref data/reference.fasta -out example</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ./bin/MindTheGap fill -graph example.h5 -bkpt example.breakpoints -out example</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ./bin/MindTheGap -help</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">In case the software does not run appropriately on your system, you should consider to install it from its source code. Retrieve the source archive file <span class="sb" style="color: #d14;">`MindTheGap-vX.Y.Z-Source.tar.gz`</span>.</span>

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<pre style="margin: 0;"> <span id="LC55" 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">@@ -65,13 +62,19 @@ In case the software does not run appropriately on your system, you should consi</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Using conda or docker</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown">MindTheGap is also distributed as a <span class="p">[</span><span class="nv" style="color: #008080;">Bioconda package</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/mindthegap</span><span class="p">)</span>:</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;">    conda install -c bioconda mindthegap</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown">Or pull the docker image of MindTheGap (warning: need to be updated with latest releases):</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;">    docker pull clemaitr/mindthegap</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Small run example</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown">MindTheGap find -in data/reads_r1.fastq,data/reads_r2.fastq -ref data/reference.fasta -out example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown">MindTheGap fill -graph example.h5 -bkpt example.breakpoints -out example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,21 +197,26 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>

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<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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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </span></span>

</pre>

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<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>

</pre>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="markdown">  <span class="idiff left right">  </span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown">  </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">    <span class="sb" style="color: #d14;">`MindTheGap find`</span> generates the following output files:</span>

</pre>

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

</pre>

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<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>

</pre>

</td>

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<td class="old_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">

200

</td>

<td class="new_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC200" 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 and deletion events.</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="markdown"><span class="p">    </span></span>

</pre>

</td>

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<td class="old_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">

</td>

<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="markdown"><span class="p">*</span> a variant file (<span class="sb" style="color: #d14;">`.othervariants.vcf`</span>) in vcf format. It contains SNPs and deletion events.</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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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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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown">    <span class="sb" style="color: #d14;">`MindTheGap fill`</span> generates the following output files:</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

203

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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="LC203" 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. </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

208

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

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="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. </span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="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">

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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></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

205

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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

211

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<pre style="margin: 0;"> <span id="LC211" 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. </span>

</pre>

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<td class="old_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">

206

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<td class="new_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC206" class="line" lang="markdown"><span class="p">  <span class="idiff left right">  </span></span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="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></span>

</pre>

</td>

</tr>

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<td class="old_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="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> 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>

</pre>

</td>

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<td class="old_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">

208

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC208" class="line" lang="markdown"><span class="p">  <span class="idiff left right">  </span></span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="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></span>

</pre>

</td>

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<td class="old_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

</td>

<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

215

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

<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>

</pre>

</td>

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<td class="old_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="new_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC210" class="line" lang="markdown">    </span>

</pre>

</td>

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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="216" style="width: 35px; color: rgba(0,0,0,0.3); 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>

</pre>

</td>

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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">

</td>

<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">

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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></span>

</pre>

</td>

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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="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown">  </span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown">      </span>

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

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown">Other optional parameters and details on input and output file formats are given in <span class="p">[</span><span class="nv" style="color: #008080;">doc/MindTheGap_insertion_caller.md</span><span class="p">](</span><span class="sx" style="color: #d14;">doc/MindTheGap_insertion_caller.md</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">doc/MindTheGap_assembly.md</span><span class="p">](</span><span class="sx" style="color: #d14;">doc/MindTheGap_assembly.md</span><span class="p">)</span>, depending on the usage.</span>

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

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<li id="1dd61bb768b613b358467981e3d64ec6394b090d">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#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">@@ -49,6 +49,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>

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<pre style="margin: 0;"> <span id="LC49" 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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<pre style="margin: 0;"> <span id="LC50" 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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<pre style="margin: 0;"> <span id="LC51" 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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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">      *</span> <span class="sb" style="color: #d14;">`-fwd-only`</span>: if set, inserted sequences are searched in only one direction : from the left kmer to the right kmer. Default behavior : not set, ie. when no solution is found in the forward direction, a solution is searched in the opposite direction (revcomp(right) --> revcomp(left)).</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="p">      </span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="p">6.</span> <span class="gs" style="font-weight: 600;">**MindTheGap Output**</span></span>

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<pre style="margin: 0;"> <span id="LC55" 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">@@ -92,7 +93,7 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;">      For insertion variants (`insertions.vcf` file only), positions are **left-normalized**. This happens when there is a small (typically <5bp)) repeated sequence between the breakpoint site and one extremity of the inserted sequence. In this case, multiple positions are possible. Here, the leftmost position is reported and the number of possible positions is indicated in the INFO field (NPOS id). This latter value is at least the size of the repeated sequence + 1 (>= fuzzy +1). </span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"><span class="sb" style="color: #d14;">      </span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;">              chr4    618791     bkpt20  T    TAGGTGTATTTAGCTCCG   .       PASS    TYPE=INS;LEN=17;QUAL=50;NSOL=1;NPOS=4;AVK=22.71;MDK=23.00      GT      1/1</span></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right"> </span>   #there are 4 (NPOS) possible positions for an insertion of 17 nt from positions 618791 to 618794 on chr4, therefore the repeat is of size 3 and is AGG.</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="sb" style="color: #d14;">              #there are 4 (NPOS) possible positions for an insertion of 17 nt from positions 618791 to 618794 on chr4, therefore the repeat is of size 3 and is AGG.</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;">      </span></span>

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<pre style="margin: 0;"> <span id="LC98" 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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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;">      </span></span>

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<br>

</li>

<li id="adece0878a8a457c3376d5aaf5b9a31d65f26181">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#adece0878a8a457c3376d5aaf5b9a31d65f26181"><strong>src/Filler.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +64,8 @@ Filler::Filler ()  : Tool ("MindTheGap fill") , _progress(0)</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp">    <span class="n" style="color: #333;">_breakpointMode</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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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp">    <span class="n" style="color: #333;">_contig_trim_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp">    <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">    <span class="n" style="color: #333;">_fwd_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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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">    <span class="n" style="color: #333;">_extend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); 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="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,7 +84,8 @@ Filler::Filler ()  : Tool ("MindTheGap fill") , _progress(0)</td>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">    <span class="n" style="color: #333;">generalParser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_front</span> <span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionOneParam</span> <span class="p">(</span><span class="n" style="color: #333;">STR_NB_CORES</span><span class="p">,</span>    <span class="s" style="color: #d14;">"number of cores"</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span>  <span class="p">));</span></span>

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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="n" style="color: #333;">IOptionsParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inputParser</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionsParser</span><span class="p">(</span><span class="s" style="color: #d14;">"Input / output"</span><span class="p">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_FILTER</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not output low quality insertions"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_EXTEND</span><span class="p">,</span> <span class="s" style="color: #d14;">"output first-contig extensions of failed gap-fillings in a separate file"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_FILTER</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not output low quality insertions (bkpt mode)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>

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<td class="old_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="new_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_CONTIG_OVERLAP</span><span class="p">,</span> <span class="s" style="color: #d14;">"Overlap between input contigs (default, ie. 0 = kmer size)"</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">));</span></span>

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<td 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">

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<td class="new_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_URI_OUTPUT</span><span class="p">,</span> <span class="s" style="color: #d14;">"prefix for output files"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">));</span></span>

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<td class="old_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">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">    <span class="n" style="color: #333;">inputParser</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_URI_BKPT</span><span class="p">,</span> <span class="s" style="color: #d14;">"breakpoint file"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</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="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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,6 +96,7 @@ Filler::Filler ()  : Tool ("MindTheGap fill") , _progress(0)</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">    </span>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp">    <span class="n" style="color: #333;">IOptionsParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fillerParser</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">OptionsParser</span><span class="p">(</span><span class="s" style="color: #d14;">"Assembly"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//TODO HERE PUT THE FILL OPTIONS</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">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">    <span class="n" style="color: #333;">fillerParser</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_FWD_ONLY</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not try in reverse direction if no inserted sequence is assembled (bkpt mode)"</span><span class="p">,</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" 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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp">    <span class="n" style="color: #333;">fillerParser</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_DEPTH</span><span class="p">,</span> <span class="s" style="color: #d14;">"maximum length of insertions (nt)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"10000"</span><span class="p">));</span></span>

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<td class="new_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">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">    <span class="n" style="color: #333;">fillerParser</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_NODES</span><span class="p">,</span> <span class="s" style="color: #d14;">"maximum number of nodes in contig graph (nt)"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">"100"</span><span class="p">));</span></span>

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -264,7 +268,16 @@ void Filler::execute ()</td>

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<td class="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">        <span class="p">}</span></span>

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

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<td class="new_line diff-line-num" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp">  </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC271" 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_EXTEND</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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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">        <span class="n" style="color: #333;">_extend</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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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">        <span class="n" style="color: #333;">_extension_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getStr</span><span class="p">(</span><span class="n" style="color: #333;">STR_URI_OUTPUT</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".extensions.fasta"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">        <span class="n" style="color: #333;">_extension_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Cannot open file "</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_extension_file_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">    <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//Getting the breakpoint sequences</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_breakpointMode</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -298,6 +311,11 @@ void Filler::execute ()</td>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp">        <span class="n" style="color: #333;">_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" 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_FWD_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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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">        <span class="n" style="color: #333;">_fwd_only</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Now do the job</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">time_t</span> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -316,6 +334,10 @@ void Filler::execute ()</td>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp">        <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">_gfa_file</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_extend</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">        <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp">    </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We gather some info/statistics to print in stdout</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">    <span class="n" style="color: #333;">resumeParameters</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -451,6 +473,10 @@ void Filler::resumeResults(double seconds){</td>

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<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;">"assembly graph file"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">_gfa_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<td class="new_line diff-line-num" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

453

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<td class="new_line diff-line-num" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

475

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

<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;">"assembly statistics file"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">_insert_info_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

476

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

<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_extend</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

477

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

<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

478

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

<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;">"extension sequence file"</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">_extension_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

479

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

<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

454

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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

455

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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

456

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<td class="new_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

482

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

<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -507,7 +533,8 @@ public:</td>

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507

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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

533

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp">     <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

534

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<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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

509

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

535

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

<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filledSequences</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

510

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<td class="new_line diff-line-num old" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC510" class="line" lang="cpp">     <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">conc_targetSequence</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="n" style="color: #333;">reverse</span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); 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="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

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

<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">extensionSequence</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

537

</td>

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

<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp">     <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">conc_targetSequence</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="n" style="color: #333;">reverse</span><span class="p">,</span> <span class="n" style="color: #333;">extensionSequence</span> <span class="p">);</span></span>

</pre>

</td>

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

511

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<td class="new_line diff-line-num" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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

<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"></span>

</pre>

</td>

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

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

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We filter out loops (ie target = seed_Rc)</span></span>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="p">;</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -532,7 +559,10 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp">     <span class="c1" style="color: #998; font-style: italic;">// Write insertions to file</span></span>

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp">     <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeFilledBreakpoint</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span><span class="n" style="color: #333;">seedName</span><span class="p">,</span><span class="n" style="color: #333;">infostring</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp">     <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeToGFA</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span><span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span><span class="n" style="color: #333;">seedName</span><span class="p">,</span><span class="n" style="color: #333;">isRc</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp">    </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_extend</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp">        <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeExtensions</span><span class="p">(</span><span class="n" style="color: #333;">extensionSequence</span><span class="p">,</span> <span class="n" style="color: #333;">seedName</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp">     <span class="n" style="color: #333;">_nb_breakpoints</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -630,10 +660,13 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp">            <span class="n" style="color: #333;">targetDictionary</span><span class="p">.</span><span class="n" style="color: #333;">insert</span> <span class="p">({</span><span class="n" style="color: #333;">targetSequence</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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">breakpointName_R</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)});</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//_object->gapFill<span>(infostring,_tid,sourceSequence,targetSequence,filledSequences,begin_kmer_repeated,end_kmer_repeated);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp">            <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">extensionSequence</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">extensionSequenceRev</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp">            <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span>  <span class="n" style="color: #333;">extensionSequence</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp">            </span>

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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//If gap-filling failed in one direction, try the other direction (from target to source in revcomp)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC636" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">_object</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">_fwd_only</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp">                <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">revcomp_sequence</span><span class="p">(</span><span class="n" style="color: #333;">sourceSequence</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp">                <span class="n" style="color: #333;">targetDictionary</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="cpp">                <span class="n" style="color: #333;">targetDictionary</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">({</span><span class="n" style="color: #333;">targetSequence2</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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">breakpointName</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="642" style="width: 35px; color: rgba(0,0,0,0.3); 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="675" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -642,13 +675,18 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//_object->GapFill<span>(infostring,_tid,sourceSequence2,targetSequence2,filledSequences,begin_kmer_repeated,end_kmer_repeated,true);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp">                <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence2</span><span class="p">,</span> <span class="n" style="color: #333;">targetSequence2</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

678

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp">                <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gapFillFromSource</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;">infostring</span><span class="p">,</span><span class="n" style="color: #333;">_tid</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence2</span><span class="p">,</span> <span class="n" style="color: #333;">targetSequence2</span><span class="p">,</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">extensionSequenceRev</span></span><span class="p">);</span></span>

</pre>

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646

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679

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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"></span>

</pre>

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647

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680

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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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648

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681

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp"></span>

</pre>

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649

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682

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp">            <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeFilledBreakpoint</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span><span class="n" style="color: #333;">breakpointName</span><span class="p">,</span><span class="n" style="color: #333;">infostring</span><span class="p">);</span></span>

</pre>

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650

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683

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp">            <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeVcf</span><span class="p">(</span><span class="n" style="color: #333;">filledSequences</span><span class="p">,</span><span class="n" style="color: #333;">breakpointName</span><span class="p">,</span><span class="n" style="color: #333;">sourceSequence</span><span class="p">);</span></span>

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651

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684

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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"></span>

</pre>

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<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;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_extend</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp">                <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeExtensions</span><span class="p">(</span><span class="n" style="color: #333;">extensionSequence</span><span class="p">,</span> <span class="n" style="color: #333;">breakpointName</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp">                <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">revcomp_sequence</span><span class="p">(</span><span class="n" style="color: #333;">targetSequence</span><span class="p">);</span></span>

</pre>

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688

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp">                <span class="n" style="color: #333;">_object</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeExtensions</span><span class="p">(</span><span class="n" style="color: #333;">extensionSequenceRev</span><span class="p">,</span> <span class="n" style="color: #333;">breakpointName</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"_reverse"</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence2</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

689

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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652

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690

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

</pre>

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<td class="new_line diff-line-num" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// We increase the breakpoint counter.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

654

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="cpp">            <span class="n" style="color: #333;">_nb_breakpoints</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); 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="852" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -814,7 +852,7 @@ void Filler::fillAny<span>::operator () (Filler* object)</td>

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814

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852

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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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815

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<td class="new_line diff-line-num" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

853

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<pre style="margin: 0;"> <span id="LC853" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

</td>

<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

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<pre style="margin: 0;"> <span id="LC854" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

817

</td>

<td class="new_line diff-line-num old" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC817" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Filler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapFillFromSource</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">infostring</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">reverse</span><span class="idiff left right"> </span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

855

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

<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Filler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gapFillFromSource</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">infostring</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">reverse</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">extensionSequence</span></span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<pre style="margin: 0;"> <span id="LC856" 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;">ModelCanonical</span> <span class="n" style="color: #333;">ModelCanonical</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

</td>

<td class="new_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

857

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

<pre style="margin: 0;"> <span id="LC857" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<td class="new_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

858

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

<pre style="margin: 0;"> <span id="LC858" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); 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="1015" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -977,6 +1015,10 @@ void Filler::gapFillFromSource(std::string & infostring, int tid, string sourceS</td>

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<td class="old_line diff-line-num" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

977

</td>

<td class="new_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

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

<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp">        <span class="n" style="color: #333;">infostring</span> <span class="o" style="font-weight: 600;">+=</span>   <span class="n" style="color: #333;">Stringify</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">format</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d"</span><span class="p">,</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

978

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<td class="new_line diff-line-num" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

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

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

979

</td>

<td class="new_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

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

<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp">     <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1018

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

<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">// no solution</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1019

</td>

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

<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1020

</td>

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

<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp">        <span class="n" style="color: #333;">extensionSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_first_contig</span><span class="p">(</span><span class="n" style="color: #333;">contig_file_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1021

</td>

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

<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

980

</td>

<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

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<td class="new_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1023

</td>

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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp">    <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">contig_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

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<td class="new_line diff-line-num" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp">    <span class="n" style="color: #333;">remove</span><span class="p">((</span><span class="n" style="color: #333;">contig_graph_file_prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".graph"</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); 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="1272" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1230,6 +1272,24 @@ void Filler::writeToGFA(std::vector<filled_insertion_t>& filledSequences, string</td>

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<td class="old_line diff-line-num" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1230

</td>

<td class="new_line diff-line-num" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1272

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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="cpp">    <span class="n" style="color: #333;">funlockfile</span><span class="p">(</span><span class="n" style="color: #333;">_gfa_file</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1231

</td>

<td class="new_line diff-line-num" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1273

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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1232

</td>

<td class="new_line diff-line-num" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1274

</td>

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

<pre style="margin: 0;"> <span id="LC1274" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1275

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

<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Filler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeExtensions</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">contigSeq</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seedName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1276

</td>

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

<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1277

</td>

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

<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1278

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

<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">llen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contigSeq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1279

</td>

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

<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1280

</td>

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

<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">llen</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1281

</td>

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

<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp">        <span class="n" style="color: #333;">flockfile</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1282

</td>

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

<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1283

</td>

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

<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//writing sequence header</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1284

</td>

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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp">        <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span><span class="p">,</span><span class="s" style="color: #d14;">">%s_len_%d source=%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">seedName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">llen</span><span class="p">,</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1285

</td>

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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//writing DNA sequence</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1286

</td>

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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp">        <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span><span class="p">,</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 class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">llen</span><span class="p">,</span><span class="n" style="color: #333;">contigSeq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1287

</td>

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

<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1288

</td>

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

<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp">        <span class="n" style="color: #333;">funlockfile</span><span class="p">(</span><span class="n" style="color: #333;">_extension_file</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1289

</td>

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

<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1290

</td>

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

<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1291

</td>

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

<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1292

</td>

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

<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1233

</td>

<td class="new_line diff-line-num" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1293

</td>

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

<pre style="margin: 0;"> <span id="LC1293" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1234

</td>

<td class="new_line diff-line-num" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1294

</td>

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

<pre style="margin: 0;"> <span id="LC1294" class="line" lang="cpp"><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">info_node_t</span> <span class="o" style="font-weight: 600;">></span>  <span class="n" style="color: #333;">Filler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">find_nodes_containing_multiple_R</span><span class="p">(</span><span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">linear_seqs_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_mis_allowed</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_gaps_allowed</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

</td>

<td class="new_line diff-line-num" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1295

</td>

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

<pre style="margin: 0;"> <span id="LC1295" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); 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="1376" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1316,3 +1376,32 @@ set< info_node_t >  Filler::find_nodes_containing_multiple_R(bkpt_dict_t targetD</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1316

</td>

<td class="new_line diff-line-num" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1376

</td>

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

<pre style="margin: 0;"> <span id="LC1376" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">Nodes</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1317

</td>

<td class="new_line diff-line-num" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1377

</td>

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

<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">terminal_nodes</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1318

</td>

<td class="new_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1378

</td>

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

<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1379

</td>

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

<pre style="margin: 0;">+<span id="LC1379" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1380

</td>

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

<pre style="margin: 0;">+<span id="LC1380" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1381

</td>

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

<pre style="margin: 0;">+<span id="LC1381" class="line" lang="cpp"><span class="n" style="color: #333;">string</span>  <span class="n" style="color: #333;">Filler</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_first_contig</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">contig_file_name</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1382

</td>

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

<pre style="margin: 0;">+<span id="LC1382" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1383

</td>

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

<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankFasta</span><span class="p">((</span><span class="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;">contig_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1384

</td>

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

<pre style="margin: 0;">+<span id="LC1384" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1385

</td>

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

<pre style="margin: 0;">+<span id="LC1385" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">contigseq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1386

</td>

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

<pre style="margin: 0;">+<span id="LC1386" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">contiglen</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1387

</td>

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

<pre style="margin: 0;">+<span id="LC1387" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1388

</td>

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

<pre style="margin: 0;">+<span id="LC1388" class="line" lang="cpp">    <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span>  <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">itSeq</span>  <span class="o" style="font-weight: 600;">=</span>  <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BankFasta</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Iterator</span>  <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">contigs</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1389

</td>

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

<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1390

</td>

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

<pre style="margin: 0;">+<span id="LC1390" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We loop over sequences.</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1391

</td>

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

<pre style="margin: 0;">+<span id="LC1391" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">();</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isDone</span><span class="p">();</span> <span class="n" style="color: #333;">itSeq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">())</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1392

</td>

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

<pre style="margin: 0;">+<span id="LC1392" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1393

</td>

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

<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp">        <span class="n" style="color: #333;">contiglen</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;">itSeq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDataSize</span><span class="p">();</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1394

</td>

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

<pre style="margin: 0;">+<span id="LC1394" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//cout << contiglen << endl;</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1395

</td>

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

<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">contiglen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_kmerSize</span> <span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1396

</td>

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

<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1397

</td>

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

<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp">            <span class="n" style="color: #333;">contigseq</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="n" style="color: #333;">itSeq</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDataBuffer</span><span class="p">(),</span><span class="n" style="color: #333;">contiglen</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1398

</td>

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

<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//cout << "contig:"<< contigseq << endl;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1399

</td>

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

<pre style="margin: 0;">+<span id="LC1399" class="line" lang="cpp">            <span class="n" style="color: #333;">contigseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contigseq</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">_kmerSize</span><span class="p">,</span> <span class="n" style="color: #333;">contiglen</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1400

</td>

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

<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1401

</td>

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

<pre style="margin: 0;">+<span id="LC1401" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1402

</td>

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

<pre style="margin: 0;">+<span id="LC1402" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1403

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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="cpp">    </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1404

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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">itSeq</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1405

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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">contigs</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">contigseq</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="7dee9a67d61921d9c899a1345a2272b965b1fde4">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#7dee9a67d61921d9c899a1345a2272b965b1fde4"><strong>src/Filler.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,8 @@ static const char* STR_URI_BKPT = "-bkpt";</td>

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37

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<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_MAX_DEPTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-max-length"</span><span class="p">;</span></span>

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38

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38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="k" style="font-weight: 600;">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_NODES</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-max-nodes"</span><span class="p">;</span></span>

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39

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39

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<pre style="margin: 0;"> <span id="LC39" 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_FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-filter"</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="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_FWD_ONLY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-fwd-only"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" 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_EXTEND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-extend"</span><span class="p">;</span></span>

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40

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">info_node_t</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); 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="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,6 +131,15 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//output file with statistics about each attempt of gap-filling</span></span>

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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_insert_info_file_name</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" 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;">_insert_info_file</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//output file in vcf format (bkpt mode)</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_vcf_file_name</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC137" 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;">_vcf_file</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//output file for single-contig extensions (-extend option)</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_extension_file_name</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC141" 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;">_extension_file</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_extend</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//parameters for dbg traversal (stop criteria)</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_max_depth</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,11 +152,13 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//parameter for gap-filling between contigs</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_contig_trim_size</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//parameter for filtering out low quality insertions</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//parameter for filtering out low quality insertions<span class="idiff left right"> (in vcf output, bkpt mode only)</span></span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_filter</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">    </span>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); 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="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">_vcf_file_name</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" 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;">_vcf_file</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//parameter for constraining assembly in the forward direction only (bkpt mode only), otherwise (default behavior) tries the revcomp direction when no inserted sequence is assembled in forward.</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_fwd_only</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC163" 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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<pre style="margin: 0;"> <span id="LC164" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,6 +174,11 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeVcf</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">breakpointName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seedk</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** writes a given extension sequence in the output extension file (fasta format)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    */</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeExtensions</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">contigSeq</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seedName</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">    </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Fill one gap</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/*template<size_t span></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">@@ -168,7 +186,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                 ,bool reversed =false);*/</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC188" 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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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">gapFillFromSource</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">infostring</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">reverse</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">gapFillFromSource</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">infostring</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sourceSequence</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filled_insertion_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">filledSequences</span><span class="p">,</span> <span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_anchor_repeated</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">reverse</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">extensionSequence</span></span> <span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp">    <span class="n" style="color: #333;">gatb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IteratorListener</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_progress</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">info_node_t</span> <span class="o" style="font-weight: 600;">></span>  <span class="n" style="color: #333;">find_nodes_containing_R</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">targetSequence</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">linear_seqs_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_mis_allowed</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_gaps_allowed</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">anchor_is_repeated</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">info_node_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">find_nodes_containing_multiple_R</span><span class="p">(</span><span class="n" style="color: #333;">bkpt_dict_t</span> <span class="n" style="color: #333;">targetDictionary</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">linear_seqs_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_mis_allowed</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_gaps_allowed</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     returns the first contig from the local assembly (only if >_kmer_size), when no solution is found, it can be returned as a safe extension.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="old_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">

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

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span>  <span class="n" style="color: #333;">get_first_contig</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">contig_file_name</span><span class="p">);</span></span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** Handle on the progress information. */</span></span>

</pre>

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<td class="old_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">

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setProgress</span> <span class="p">(</span><span class="n" style="color: #333;">gatb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IteratorListener</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">progress</span><span class="p">)</span>  <span class="p">{</span> <span class="n" style="color: #333;">SP_SETATTR</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">);</span> <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"></span>

</pre>

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<li id="b958235ee8db37bcaceda04b6d55553b450c2db4">

<a href="https://salsa.debian.org/med-team/mindthegap/-/commit/b7bdcbee246d474229b51a2960c60e0f6caaf96c#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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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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>

</pre>

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); 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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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;">"2.2.<span class="idiff left right">2</span>"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); 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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="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;">"2.2.<span class="idiff left right">3</span>"</span><span class="p">;</span></span>

</pre>

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

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

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); 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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); 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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="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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