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GitLab

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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1">65c61e44</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-04-26T15:25:17+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1.0</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">

CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#4a8486805915245bbbe2e3c8c1a9d680c6843a82">

LICENSE.md

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">

src/CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#9d51a78783295e039ae9dbc298d048f0c6e01b63">

src/Flexbar.cpp

</a>

</li>

<li class="file-stats">

<a href="#e46cbf6df1dcc17df0ea6052697f523aefb88ff4">

src/FlexbarTypes.h

</a>

</li>

<li class="file-stats">

<a href="#1bee0e946e884ffe0c4bcf077071fc24e8887d09">

src/Options.h

</a>

</li>

<li class="file-stats">

<a href="#5892684acbf66442a550859d89842772d4e04d36">

src/PairedOutput.h

</a>

</li>

<li class="file-stats">

<a href="#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd">

src/SeqAlign.h

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ cmake_minimum_required( VERSION 2.8.2 )</td>

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

2

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2

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

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

</pre>

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

3

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span> FLEXBAR <span class="p">)</span></span>

</pre>

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

4

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4

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

</pre>

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

5

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SEQAN_APP_VERSION <span class="s2" style="color: #d14;">"3.<span class="idiff left right">0.3</span>"</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SEQAN_APP_VERSION <span class="s2" style="color: #d14;">"3.<span class="idiff left right">1.0</span>"</span> <span class="p">)</span></span>

</pre>

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6

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

</pre>

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

7

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">FLEXBAR_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include <span class="p">)</span></span>

</pre>

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

8

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># link_directories( ${FLEXBAR_SOURCE_DIR}/lib )</span></span>

</pre>

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<br>

</li>

<li id="4a8486805915245bbbe2e3c8c1a9d680c6843a82">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#4a8486805915245bbbe2e3c8c1a9d680c6843a82"><strong>LICENSE.md</strong></a>

<hr>

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown">BSD 3-Clause License</span>

</pre>

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

2

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

2

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

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">Copyright (c) 201<span class="idiff left right">7</span>, SeqAn</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Copyright (c) 201<span class="idiff left right">8</span>, SeqAn</span>

</pre>

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

4

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

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">All rights reserved.</span>

</pre>

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

5

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

5

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

</pre>

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

6

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

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown">Redistribution and use in source and binary forms, with or without</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Flexbar <span class="idiff left right">—</span> flexible barcode and adapter removal</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Flexbar <span class="idiff left right">–</span> flexible barcode and adapter removal</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. <span class="idiff left right">It supports next-generation sequencing data in fasta and fastq format, e.g. from Roche 454 and</span> the Illumina platform.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. <span class="idiff left right">Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fasta and fastq format, e.g. from</span> the Illumina platform.</span>

</pre>

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

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC5" class="line" lang="markdown">Refer to the <span class="p">[</span><span class="nv" style="color: teal;">manual</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki</span><span class="p">)</span> or contact <span class="p">[</span><span class="nv" style="color: teal;"><span class="idiff left right">jtr</span>oehr</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jtroehr</span><span class="p">)</span> for support with this application.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">Refer to the <span class="p">[</span><span class="nv" style="color: teal;">manual</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki</span><span class="p">)</span> or contact <span class="p">[</span><span class="nv" style="color: teal;"><span class="idiff left right">Johannes R</span>oehr</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jtroehr</span><span class="p">)</span> for support with this application.</span>

</pre>

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: teal;">Flexbar logo</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki/images/flexbar-logo.png</span><span class="p">)</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Reference</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Reference<span class="idiff left right">s</span></span></span>

</pre>

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

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="idiff left right">Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="idiff left right">Johannes T. Roehr, Christoph Dieterich, Knut Reinert: Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017</span>.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC14" class="line" lang="markdown">See article on <span class="p">[</span><span class="nv" style="color: teal;">PubMed</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/pubmed/24832523</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">See article on <span class="p">[</span><span class="nv" style="color: teal;">PubMed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pubmed/28541403</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">See article on <span class="p">[</span><span class="nv" style="color: teal;">PubMed</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/pubmed/24832523</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Download</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); 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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,25 +25,25 @@ Flexbar source code as well as binaries for Linux and Mac OS can be downloaded o</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Building from source</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">Make sure that <span class="sb" style="color: #d14;">`cmake`</span> is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). <span class="idiff left right">Using a package manager is a simple way to install them</span>. Furthermore, the SeqAn library and a compiler that supports C++14 is required:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">Make sure that <span class="sb" style="color: #d14;">`cmake`</span> is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). <span class="idiff left">For example on Debian systems, install the packages </span><span class="sb" style="color: #d14;"><span class="idiff">`libtbb-dev`</span></span><span class="idiff"> and </span><span class="sb" style="color: #d14;"><span class="idiff right">`libtbb2`</span></span>. Furthermore, the SeqAn library and a compiler that supports C++14 is required:</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">*</span> Get SeqAn library version 2.2.0 <span class="p">[</span><span class="nv" style="color: teal;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/seqan/releases/download/seqan-v2.2.0/seqan-library-2.2.0.tar.xz</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line 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="LC27" class="line" lang="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">0.3</span> source code <span class="p">[</span><span class="nv" style="color: teal;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" 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="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">1</span> source code <span class="p">[</span><span class="nv" style="color: teal;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new_line" 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="markdown">Decompress both files:</span>

</pre>

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<td class="diff-line-num new_line" 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">

34

</td>

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

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

</pre>

</td>

</tr>

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

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

31

</td>

<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right"> tar xzf flexbar-3.0.3</span>.tar.gz</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

</td>

<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right"> </span>tar xJf seqan-library-2.2.0.tar.xz</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

35

</td>

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right">tar xzf flexbar-3.1.0</span>.tar.gz</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

</td>

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;">      tar xJf seqan-library-2.2.0.tar.xz</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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">

33

</td>

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

37

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" 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">

34

</td>

<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

</td>

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

<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">Move SeqAn include folder to Flexbar:</span>

</pre>

</td>

</tr>

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

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

35

</td>

<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

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

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

</pre>

</td>

</tr>

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

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

36

</td>

<td class="diff-line-num new_line old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        mv seqan-library-2.2.0/include flexbar-3.0.3</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

40

</td>

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       mv seqan-library-2.2.0/include flexbar-3.1.0</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

37

</td>

<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

</td>

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

42

</td>

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

<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown">Use these commands for building:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

</td>

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

43

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        cd flexbar-3.0.3</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        </span>cmake .</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

</td>

<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        </span>make</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

</td>

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

<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       cd flexbar-3.1.0</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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

<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       </span>cmake .</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

</td>

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

<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       </span>make</span></span>

</pre>

</td>

</tr>

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

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

43

</td>

<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

</td>

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

<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

44

</td>

<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

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

<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown">Flexbar version 2.7 requires SeqAn 2.1.1 instead. Releases prior to 2.7 use the SeqAn 1.4.2 library.</span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC49" 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">@@ -51,19 +55,19 @@ For execution of provided Flexbar binaries, the corresponding TBB library has to</td>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Linux</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">Adjust lib search path to include the absolute path of the Flexbar directory containing the lib file libtbb.so.2 for the current terminal session, or permanently in shell startup scripts:</span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        </span>export LD_LIBRARY_PATH=/path/FlexbarDir:$LD_LIBRARY_PATH</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       </span>export LD_LIBRARY_PATH=/path/FlexbarDir:$LD_LIBRARY_PATH</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Mac OS</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown">It applies the same as for Linux. Make the file libtbb.dylib available by setting the lib search path:</span>

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

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        </span>export DYLD_LIBRARY_PATH=/path/FlexbarDir:$DYLD_LIBRARY_PATH</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       </span>export DYLD_LIBRARY_PATH=/path/FlexbarDir:$DYLD_LIBRARY_PATH</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Program usage</span></span>

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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">Flexbar needs at least one file with sequencing reads in fasta or fastq format as input. Additionally, the target name and further options can be specified. For read separation based on barcodes and for adapter removal, a file in fasta format with barcode or adapter sequences should be provided.</span>

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

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">        </span>flexbar -r reads [-b barcodes] [-a adapters] [options]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">       </span>flexbar -r reads [-b barcodes] [-a adapters] [options]</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">Refer to the help screen <span class="sb" style="color: #d14;">`flexbar -h`</span> or <span class="p">[</span><span class="nv" style="color: teal;">manual</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki</span><span class="p">)</span> for more information. Although default parameters of Flexbar are optimized to deliver good results in many scenarios, the adjustment of parameters might improve results, e.g. <span class="sb" style="color: #d14;">`--adapter-min-overlap`</span>. To run tests, make sure <span class="sb" style="color: #d14;">`flexbar`</span> is reachable via the path variable and run <span class="sb" style="color: #d14;">`flexbar_test.sh`</span> within the test folder.</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">@@ -71,11 +75,11 @@ Refer to the help screen `flexbar -h` or [manual](https://github.com/seqan/flexb</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown">In this example, reads that are barcoded on left side are demultiplexed by specifying a file with barcodes in fasta format. After separation of reads, given adapters are removed from the right side if they do not align before read start. The left side of reads is kept if long enough. Remaining reads are written to the file <span class="sb" style="color: #d14;">`target.fastq`</span> in same format as the input.</span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right"> </span>flexbar -r reads.fq -t target -b brc.fa -be LTAIL -a adp.fa</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;">      flexbar -r reads.fq -t target -b brc.fa -be LTAIL -a adp.fa</span></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">The second example shows how to trim compressed reads based on their quality scores in illumina version 1.8 format. Afterwards, provided adapters are removed in right trim-end mode, only if the overlap of adapter and read has at least length five with at most 40% errors.</span>

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

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <span class="idiff left right"> </span>flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.4</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;">      flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.4</span></span>

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

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">For further examples visit the <span class="p">[</span><span class="nv" style="color: teal;">manual</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki</span><span class="p">)</span> page.</span>

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

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<br>

</li>

<li id="631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7"><strong>src/CMakeLists.txt</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">@@ -59,12 +59,3 @@ endif()</td>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># endif()</span></span>

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60

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SEQAN_CTD_EXECUTABLES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SEQAN_CTD_EXECUTABLES</span><span class="si" style="color: #d14;">}</span> flexbar CACHE INTERNAL <span class="s2" style="color: #d14;">""</span> <span class="p">)</span></span></pre>

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62

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="cmake"></span>

</pre>

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

63

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># set( CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "/Users/jtr/Downloads/seqan-trunk/util/cmake" )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

64

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># set( SEQAN_FIND_DEPENDENCIES ZLIB BZip2 )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

65

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC65" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># find_package( SeqAn REQUIRED )</span></span>

</pre>

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66

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC66" class="line" lang="cmake"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

67

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC67" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># add_definitions( ${SEQAN_DEFINITIONS} )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

68

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC68" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># include_directories( ${SEQAN_INCLUDE_DIRS} )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC69" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># target_link_libraries( flexbar ${SEQAN_LIBRARIES} )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

70

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># set( SEQAN_HAS_ZLIB FALSE )</span></span></pre>

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<br>

</li>

<li id="9d51a78783295e039ae9dbc298d048f0c6e01b63">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#9d51a78783295e039ae9dbc298d048f0c6e01b63"><strong>src/Flexbar.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">@@ -2,7 +2,7 @@</td>

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

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

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   </span></span>

</pre>

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

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   Flexbar - flexible barcode and adapter removal</span></span>

</pre>

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

4

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

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   </span></span>

</pre>

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

5

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   Version 3.<span class="idiff left right">0.3</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   Version 3.<span class="idiff left right">1.0</span></span></span>

</pre>

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

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

6

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

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

</pre>

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

7

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   uses SeqAn library release 2.2.0</span></span>

</pre>

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

8

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

8

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   and TBB library 4.0 or later</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,8 +27,8 @@ int main(int argc, const char* argv[]){</td>

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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>

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<pre style="margin: 0;"> <span id="LC28" 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;">seqan</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"3.<span class="idiff left right">0.3</span>"</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">date</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">May 2017</span>"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"3.<span class="idiff left right">1</span>"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">date</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">April 2018</span>"</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">   <span class="n" style="color: #333;">ArgumentParser</span> <span class="n" style="color: #333;">parser</span><span class="p">(</span><span class="s" style="color: #d14;">"flexbar"</span><span class="p">);</span></span>

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

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<br>

</li>

<li id="e46cbf6df1dcc17df0ea6052697f523aefb88ff4">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#e46cbf6df1dcc17df0ea6052697f523aefb88ff4"><strong>src/FlexbarTypes.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,17 +9,19 @@ class SeqRead {</td>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c">     <span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c">     <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c">     <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c">     <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">umi</span></span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c">     <span class="n" style="color: #333;">SeqRead</span><span class="p">(</span><span class="n" style="color: #333;">TSeqStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">TString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seqID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c">             <span class="n" style="color: #333;">seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c">             <span class="n" style="color: #333;">id</span><span class="p">(</span><span class="n" style="color: #333;">seqID</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC16" class="line" lang="c">             <span class="n" style="color: #333;">id</span><span class="p">(</span><span class="n" style="color: #333;">seqID</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c">             <span class="n" style="color: #333;">umi</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">     </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c">     <span class="n" style="color: #333;">SeqRead</span><span class="p">(</span><span class="n" style="color: #333;">TSeqStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">TString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seqID</span><span class="p">,</span> <span class="n" style="color: #333;">TString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">quality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c">             <span class="n" style="color: #333;">seq</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">             <span class="n" style="color: #333;">id</span><span class="p">(</span><span class="n" style="color: #333;">seqID</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC22" class="line" lang="c">             <span class="n" style="color: #333;">qual</span><span class="p">(</span><span class="n" style="color: #333;">quality</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC23" class="line" lang="c">             <span class="n" style="color: #333;">qual</span><span class="p">(</span><span class="n" style="color: #333;">quality</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC24" class="line" lang="c">             <span class="n" style="color: #333;">umi</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="c"></span>

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<br>

</li>

<li id="1bee0e946e884ffe0c4bcf077071fc24e8887d09">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#1bee0e946e884ffe0c4bcf077071fc24e8887d09"><strong>src/Options.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); 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="17" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -17,13 +17,14 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">readsFile</span><span class="p">,</span> <span class="n" style="color: #333;">readsFile2</span><span class="p">,</span> <span class="n" style="color: #333;">barReadsFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">barcodeFile</span><span class="p">,</span> <span class="n" style="color: #333;">adapterFile</span><span class="p">,</span> <span class="n" style="color: #333;">barcode2File</span><span class="p">,</span> <span class="n" style="color: #333;">adapter2File</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">adapterSeq</span><span class="p">,</span> <span class="n" style="color: #333;">targetName</span><span class="p">,</span> <span class="n" style="color: #333;">logAlignStr</span><span class="p">,</span> <span class="n" style="color: #333;">outCompression</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC20" class="line" lang="c">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">,</span> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c">     </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">useAdapterFile</span><span class="p">,</span> <span class="n" style="color: #333;">useNumberTag</span><span class="p">,</span> <span class="n" style="color: #333;">useRemovalTag</span><span class="p">,</span> <span class="n" style="color: #333;">randTag</span><span class="p">,</span> <span class="n" style="color: #333;">logStdout</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">switch2Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">writeUnassigned</span><span class="p">,</span> <span class="n" style="color: #333;">writeSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">writeSingleReadsP</span><span class="p">,</span> <span class="n" style="color: #333;">writeLengthDist</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC23" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useStdin</span><span class="p">,</span> <span class="n" style="color: #333;">useStdout</span><span class="p">,</span> <span class="n" style="color: #333;">relaxRegion</span><span class="p">,</span> <span class="n" style="color: #333;">revCompAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimPostRm</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bNoMBV</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useStdin</span><span class="p">,</span> <span class="n" style="color: #333;">useStdout</span><span class="p">,</span> <span class="n" style="color: #333;">relaxRegion</span><span class="p">,</span> <span class="n" style="color: #333;">revCompAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimPostRm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutLen_begin</span><span class="p">,</span> <span class="n" style="color: #333;">cutLen_end</span><span class="p">,</span> <span class="n" style="color: #333;">cutLen_read</span><span class="p">,</span> <span class="n" style="color: #333;">a_tail_len</span><span class="p">,</span> <span class="n" style="color: #333;">b_tail_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimWinSize</span><span class="p">,</span> <span class="n" style="color: #333;">a_overhang</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimWinSize</span><span class="p">,</span> <span class="n" style="color: #333;">a_overhang</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hpsMinLength</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxUncalled</span><span class="p">,</span> <span class="n" style="color: #333;">min_readLen</span><span class="p">,</span> <span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">nThreads</span><span class="p">,</span> <span class="n" style="color: #333;">bundleSize</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">b_gapCost</span><span class="p">;</span></span>

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,6 +54,8 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c">             <span class="n" style="color: #333;">barcode2File</span>   <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c">             <span class="n" style="color: #333;">adapter2File</span>   <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c">             <span class="n" style="color: #333;">outCompression</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c">             <span class="n" style="color: #333;">trimLeftNucs</span>   <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c">             <span class="n" style="color: #333;">trimRightNucs</span>  <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c">             </span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c">             <span class="n" style="color: #333;">isPaired</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="LC61" class="line" lang="c">             <span class="n" style="color: #333;">useAdapterFile</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +73,6 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c">             <span class="n" style="color: #333;">relaxRegion</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="LC74" class="line" lang="c">             <span class="n" style="color: #333;">revCompAdapter</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="LC75" class="line" lang="c">             <span class="n" style="color: #333;">qtrimPostRm</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="LC73" class="line" lang="c">             <span class="n" style="color: #333;">bNoMBV</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="LC76" class="line" lang="c">             </span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c">             <span class="n" style="color: #333;">cutLen_begin</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="LC78" class="line" lang="c">             <span class="n" style="color: #333;">cutLen_end</span>    <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,6 +83,8 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c">             <span class="n" style="color: #333;">b_tail_len</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="LC84" class="line" lang="c">             <span class="n" style="color: #333;">b_min_overlap</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="LC85" class="line" lang="c">             </span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c">             <span class="n" style="color: #333;">a_errorRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c">             </span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c">             <span class="n" style="color: #333;">format</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FASTA</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c">             <span class="n" style="color: #333;">qual</span>      <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SANGER</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c">             <span class="n" style="color: #333;">qTrim</span>     <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QOFF</span><span class="p">;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,13 +167,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error rate threshold for mismatches and gaps."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DOUBLE</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-keep"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Keep barcodes within reads instead of removal."</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bu"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-unassigned"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Include unassigned reads in output generation."</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("ba", "barcode-no-mbv", "Turn off bit-vector alignment with edit distance."));</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-match"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment match score."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bi"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-mismatch"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment mismatch score."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bg"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-gap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment gap score."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("bm", "barcode-match", "Alignment match score in case of no-mbv.", ARG::INTEGER));</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("bi", "barcode-mismatch", "Standard alignment mismatch score.", ARG::INTEGER));</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("bg", "barcode-gap", "Standard alignment gap score.", ARG::INTEGER));</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">    <span class="n" style="color: #333;">addSection</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"Adapter removal"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"a"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"adapters"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fasta file with adapters for removal that may contain N."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="191" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -191,6 +191,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"u"</span><span class="p">,</span> <span class="s" style="color: #d14;">"max-uncalled"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Allowed uncalled bases N for each read."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

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<td class="diff-line-num new_line" 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="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pre-trim-left"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim given number of bases on 5' read end before detection."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pre-trim-right"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim specified number of bases on 3' end prior to detection."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC194" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on the left read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC195" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"Y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on the right read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC196" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"Z"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum length of homopolymers at read ends."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim to specified read length from 3' end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"min-read-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum read length to remain after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,7 +218,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stdout-log"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Write statistics to console instead of target log file."</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"removal-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Tag reads that are subject to adapter or barcode removal."</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"number-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Replace read tags by ascending number to save space."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">d"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"random-tags"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Capture read sequence</span> at barcode or adapter N positions."</span><span class="p">));</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left">i"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"umi-tags"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Capture UMIs in reads</span> at barcode or adapter N positions."</span><span class="p">));</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c">    <span class="n" style="color: #333;">hideOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"version"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,12 +227,10 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-tail-length"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-keep"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-unassigned"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC227" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// setAdvanced(parser, "barcode-no-mbv");</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-match"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-mismatch"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-gap"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapters2"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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<td class="diff-line-num new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

235

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-tail-length"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

235

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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

236

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// setAdvanced(parser, "adapter-overhang");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,6 +240,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

239

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

240

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-mismatch"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

240

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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-gap"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

242

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

243

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

244

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

245

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

242

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<td class="diff-line-num new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

246

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

243

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-win-size"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-post-removal"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -249,7 +253,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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

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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

253

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

<pre style="margin: 0;"> <span id="LC253" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"length-dist"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

250

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"single-reads-paired"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"number-tags"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC252" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">random</span>-tags"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">    <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">umi</span>-tags"</span><span class="p">);</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c">    </span>

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

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c">    <span class="n" style="color: #333;">setCategory</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trimming"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -292,14 +296,16 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c">    <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"zip-output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GZ BZ2"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c">    <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-read-set"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1 2"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c">    </span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">,</span>          <span class="s" style="color: #d14;">"flexbarOut"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">,</span>         <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"bundle"</span><span class="p">,</span>          <span class="s" style="color: #d14;">"256"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"max-uncalled"</span><span class="p">,</span>    <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"min-read-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"18"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"flexbarOut"</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC300" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"bundle"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"256"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC302" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC303" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"max-uncalled"</span><span class="p">,</span>         <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"min-read-length"</span><span class="p">,</span>      <span class="s" style="color: #d14;">"18"</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

305

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3"</span><span class="p">);</span></span>

</pre>

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300

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<td class="diff-line-num new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

306

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

301

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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

307

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-trim-end"</span><span class="p">,</span>   <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

302

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<td class="diff-line-num new_line old" data-linenumber="308" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC302" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.<span class="idiff left right">1</span>"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

308

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.<span class="idiff left right">0</span>"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

303

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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

309

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-match"</span><span class="p">,</span>      <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

304

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<td class="diff-line-num new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

310

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-mismatch"</span><span class="p">,</span>   <span class="s" style="color: #d14;">"-1"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

305

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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

311

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

<pre style="margin: 0;"> <span id="LC311" class="line" lang="c">    <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-gap"</span><span class="p">,</span>        <span class="s" style="color: #d14;">"-9"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); 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="570" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -564,6 +570,19 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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564

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570

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"pre-trim-right:        "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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<td class="diff-line-num new_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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<td class="diff-line-num new_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

572

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

<pre style="margin: 0;"> <span id="LC572" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

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

<pre style="margin: 0;">+<span id="LC573" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">)){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

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

<pre style="margin: 0;">+<span id="LC574" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

575

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

<pre style="margin: 0;">+<span id="LC575" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-left-hps:    "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

576

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

<pre style="margin: 0;">+<span id="LC576" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">)){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

</td>

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

<pre style="margin: 0;">+<span id="LC579" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

</td>

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

<pre style="margin: 0;">+<span id="LC580" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-right-hps:   "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

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

<pre style="margin: 0;">+<span id="LC581" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

</td>

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

<pre style="margin: 0;">+<span id="LC582" class="line" lang="c">    </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

583

</td>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="c">    <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-hps-length:  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

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

586

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

<pre style="margin: 0;"> <span id="LC586" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">)){</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

</td>

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

587

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

<pre style="margin: 0;"> <span id="LC587" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

569

</td>

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

588

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

<pre style="margin: 0;"> <span id="LC588" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-length:      "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -673,7 +692,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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<td class="diff-line-num old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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

692

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

<pre style="margin: 0;"> <span id="LC692" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"length-dist"</span><span class="p">))</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeLengthDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

674

</td>

<td class="diff-line-num new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

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

<pre style="margin: 0;"> <span id="LC693" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"number-tags"</span><span class="p">))</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useNumberTag</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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">

675

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<td class="diff-line-num new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

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

<pre style="margin: 0;"> <span id="LC694" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"removal-tags"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useRemovalTag</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

676

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<td class="diff-line-num new_line old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC676" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">random-tags"</span></span><span class="p"><span class="idiff right">))</span></span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

695

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">umi-tags"</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff right">   </span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

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<td class="diff-line-num new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

678

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<td class="diff-line-num new_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

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<td class="diff-line-num new_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

698

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -716,26 +735,23 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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716

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<td class="diff-line-num new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

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<pre style="margin: 0;"> <span id="LC735" class="line" lang="c">            <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

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<pre style="margin: 0;"> <span id="LC736" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

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<td class="diff-line-num new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

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<pre style="margin: 0;"> <span id="LC737" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-unassigned"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeUnassigned</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

719

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<td class="diff-line-num new_line old" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC719" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// if(isSet(parser, "barcode-no-mbv"))     o.bNoMBV          = true;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

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<pre style="margin: 0;"> <span id="LC738" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

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<td class="diff-line-num new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

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

<pre style="margin: 0;"> <span id="LC739" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span><span class="p">,</span>    <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-match"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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

740

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

<pre style="margin: 0;"> <span id="LC740" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-mismatch"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

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

741

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<pre style="margin: 0;"> <span id="LC741" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span><span class="p">,</span>  <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-gap"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="diff-line-num new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

725

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<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC725" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// if(o.bNoMBV){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

726

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<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC726" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

727

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<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC727" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-match:        "</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

728

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<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC728" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

729

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC729" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

730

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC730" class="line" lang="c">                    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

731

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC731" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-mismatch:     "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC732" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

733

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC733" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

734

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC734" class="line" lang="c">                    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

735

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-gap:          "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

736

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC736" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

737

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC737" class="line" lang="c">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

738

</td>

<td class="diff-line-num new_line old" data-linenumber="743" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC738" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// }</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

743

</td>

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

<pre style="margin: 0;">+<span id="LC743" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-match:        "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

744

</td>

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

<pre style="margin: 0;">+<span id="LC744" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

</td>

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

<pre style="margin: 0;">+<span id="LC745" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

746

</td>

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

<pre style="margin: 0;">+<span id="LC746" class="line" lang="c">            </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

747

</td>

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

<pre style="margin: 0;">+<span id="LC747" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-mismatch:     "</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

748

</td>

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

<pre style="margin: 0;">+<span id="LC748" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

</td>

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

<pre style="margin: 0;">+<span id="LC749" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

</td>

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

<pre style="margin: 0;">+<span id="LC750" class="line" lang="c">            </span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

</td>

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

<pre style="margin: 0;">+<span id="LC751" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-gap:          "</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

</td>

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

<pre style="margin: 0;">+<span id="LC752" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

</td>

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

<pre style="margin: 0;">+<span id="LC753" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

</td>

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

<pre style="margin: 0;">+<span id="LC754" class="line" lang="c">            </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

<td class="diff-line-num new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

</td>

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

<pre style="margin: 0;"> <span id="LC755" class="line" lang="c">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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

740

</td>

<td class="diff-line-num new_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

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

<pre style="margin: 0;"> <span id="LC756" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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

741

</td>

<td class="diff-line-num new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

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

<pre style="margin: 0;"> <span id="LC757" class="line" lang="c">    </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="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -747,10 +763,10 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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

747

</td>

<td class="diff-line-num new_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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

<pre style="margin: 0;"> <span id="LC763" class="line" lang="c">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a_trim_end</span><span class="p">;</span></span>

</pre>

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

748

</td>

<td class="diff-line-num new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

764

</td>

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

<pre style="margin: 0;"> <span id="LC764" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trim-end"</span><span class="p">);</span></span>

</pre>

</td>

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

749

</td>

<td class="diff-line-num new_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

</td>

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

<pre style="margin: 0;"> <span id="LC765" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

750

</td>

<td class="diff-line-num new_line old" data-linenumber="766" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC750" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LEFT"</span><span class="p">)</span>   <span class="idiff left right">     </span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

751

</td>

<td class="diff-line-num new_line old" data-linenumber="766" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC751" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">)</span>  <span class="idiff left right">     </span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

752

</td>

<td class="diff-line-num new_line old" data-linenumber="766" style="width: 35px; color: rgba(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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC752" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ANY"</span><span class="p">)</span>    <span class="idiff left right">     </span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

753

</td>

<td class="diff-line-num new_line old" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC753" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span>  <span class="idiff left right"> </span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

766

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

<pre style="margin: 0;">+<span id="LC766" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LEFT"</span><span class="p">)</span>   <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

767

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

<pre style="margin: 0;">+<span id="LC767" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">)</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

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<pre style="margin: 0;">+<span id="LC768" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ANY"</span><span class="p">)</span>    <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

769

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

<pre style="margin: 0;">+<span id="LC769" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

754

</td>

<td class="diff-line-num new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RTAIL"</span><span class="p">)</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

</td>

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

771

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="c">            <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

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

772

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<pre style="margin: 0;"> <span id="LC772" class="line" lang="c">                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Specified adapter trim-end is unknown!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -797,7 +813,6 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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<td class="diff-line-num old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

<td class="diff-line-num new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

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<pre style="margin: 0;"> <span id="LC813" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// getOptionValue(o.a_overhang, parser, "adapter-overhang");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="diff-line-num new_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">

814

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<pre style="margin: 0;"> <span id="LC814" class="line" lang="c">            <span class="c1" style="color: #998; font-style: italic;">// *out << "adapter-overhang:      " << o.a_overhang << endl;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="diff-line-num new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

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

<pre style="margin: 0;"> <span id="LC815" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

800

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<td class="diff-line-num new_line old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC800" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

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

816

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<pre style="margin: 0;"> <span id="LC816" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span>    <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-match"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

802

</td>

<td class="diff-line-num new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

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

<pre style="margin: 0;"> <span id="LC817" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-mismatch"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

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

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="c">            <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</span><span class="p">,</span>  <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-gap"</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="5892684acbf66442a550859d89842772d4e04d36">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#5892684acbf66442a550859d89842772d4e04d36"><strong>src/PairedOutput.h</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">@@ -14,13 +14,17 @@ class PairedOutput : public tbb::filter {</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_mapsize</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">,</span> <span class="n" style="color: #333;">m_<span class="idiff left">cutLen_read</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_</span>qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeUnassigned</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeSingleReadsP</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_randTag</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c">     <span class="n" style="color: #333;">tbb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m_nSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">m_nLowPhred</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">m_target</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">,</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c">     </span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">m_errorRate</span><span class="p">;</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileFormat</span>     <span class="n" style="color: #333;">m_format</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">     <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RunType</span>        <span class="n" style="color: #333;">m_runType</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,12 +50,16 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c">             <span class="n" style="color: #333;">m_runType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">runType</span><span class="p">),</span></span>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c">             <span class="n" style="color: #333;">m_barDetect</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span><span class="p">),</span></span>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c">             <span class="n" style="color: #333;">m_minLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">min_readLen</span><span class="p">),</span></span>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c">             <span class="n" style="color: #333;">m_cutLen_read</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c">             <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c">             <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c">             <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c">             <span class="n" style="color: #333;">m_errorRate</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c">             <span class="n" style="color: #333;">m_qtrim</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qTrim</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c">             <span class="n" style="color: #333;">m_qtrimThresh</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qtrimThresh</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c">             <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qtrimWinSize</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c">             <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qtrimPostRm</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c">             <span class="n" style="color: #333;">m_isPaired</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">isPaired</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c">             <span class="n" style="color: #333;">m_randTag</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c">             <span class="n" style="color: #333;">m_writeUnassigned</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeUnassigned</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c">             <span class="n" style="color: #333;">m_writeSingleReads</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeSingleReads</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c">             <span class="n" style="color: #333;">m_writeSingleReadsP</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeSingleReadsP</span><span class="p">),</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -227,6 +235,72 @@ public:</td>

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

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">    </span>

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

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c">            </span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c">            <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c">            <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c">            </span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">            <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c">                    </span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c">                    </span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</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="LC248" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</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="LC249" class="line" lang="c">                    </span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c">                    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

251

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">                    </span>

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

253

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c">                                    <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC254" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC255" class="line" lang="c">                            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_errorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)){</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">                                    <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC257" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

258

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">                    </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</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;">cutPos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">){</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c">                            <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC263" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC264" class="line" lang="c">                                    <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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

</pre>

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

269

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c">            <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>

</pre>

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

274

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c">            <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC275" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c">            <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC277" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC279" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new new_line" 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="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="c">                    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC282" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC283" class="line" lang="c">                    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

286

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c">                                    <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

287

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

288

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c">                            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_errorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">)){</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC289" class="line" lang="c">                                    <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

290

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

291

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

292

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="c">                    </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

293

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">){</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC294" class="line" lang="c">                            <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">));</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

295

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c">            </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC296" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

297

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c">                                    <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">));</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC298" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

299

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC300" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

301

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC302" class="line" lang="c">    </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writePairedRead</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TPairedRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pRead</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c">            </span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c">            <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -245,6 +319,11 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c">                                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qualTrim</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrim</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">))</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_nLowPhred</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c">                                            <span class="p">}</span></span>

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

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimLeftNucs</span>  <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimRightNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c">                                            </span>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_randTag</span><span class="p">)</span> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c">                                            </span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c">                                                    </span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c">                                                    <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barID</span><span class="p">].</span><span class="n" style="color: #333;">f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeRead</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -276,6 +355,23 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="c">                                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qualTrim</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrim</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">))</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_nLowPhred</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

356

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC357" class="line" lang="c">                                            </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

358

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimLeftNucs</span>  <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

359

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="c">                                                    <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

360

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="c">                                                    <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

361

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

362

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimRightNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

363

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c">                                                    <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

364

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c">                                                    <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

365

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

366

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="c">                                            </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

367

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_randTag</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC368" class="line" lang="c">                                                    <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC369" class="line" lang="c">                                                    <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="c">                                                    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC371" class="line" lang="c">                                                    <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC372" class="line" lang="c">                                                    <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="c">                                            <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC374" class="line" lang="c">                                            </span>

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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">)</span> <span class="n" style="color: #333;">l1ok</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="diff-line-num old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

280

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">)</span> <span class="n" style="color: #333;">l2ok</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="LC377" class="line" lang="c">                                            </span>

</pre>

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</li>

<li id="2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd">

<a href="https://salsa.debian.org/med-team/flexbar/commit/65c61e440a3ffb44bcb473442d3a4edae781d1a1#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd"><strong>src/SeqAlign.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -234,8 +234,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// valid alignment, not neccesarily removal</span></span>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_randTag</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC237" class="line" lang="c">                            <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">id</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC238" class="line" lang="c">                            <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">id</span></span><span class="p">,</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c">                            <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">umi</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

238

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c">                            <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">umi</span></span><span class="p">,</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

239

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<td class="diff-line-num new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c">                    <span class="c1" style="color: #998; font-style: italic;">// alignment stats</span></span>

</pre>

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