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GitLab

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<h3>

Andreas Tille pushed to branch master

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/4c5fb0505cefa6300f8011db975946bd7b156b6e">4c5fb050</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.5.0</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/8c3c7d6d388708115b6d25ec46b55c4d4b3b3836">8c3c7d6d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.5.0'

Update to upstream version '3.5.0'

with Debian dir bc3bcbc1bbdb48456fa875da4341399a4e8720b6</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/5f6dbc479c7e7c0e2e6f3bd107fb488a3e1f1796">5f6dbc47</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:45Z</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/d8d716bf99cc60bc54ee21164711993f6c4850a5">d8d716bf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/70bbf50e5d08e46ae242bec06aa12bc759ef7a9f">70bbf50e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:50Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/ee7802787c43099bdf209ec8c19eaa886edb3019">ee780278</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:27:50Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/299261d2beec41d20ce41e1701d01b302a72daa7">299261d2</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-07-27T19:30:28Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>18 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">

CMakeLists.txt

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<span class="deleted-file">

−

debian/compat

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#648cfa9d8fd7911c362a25c7df65fc8d476d8734">

<span class="new-file">

+

galaxy/flexbar.pl

</span>

</a>

</li>

<li class="file-stats">

<a href="#d33b186e083bbba7569fc40cb94aba122a125c93">

<span class="new-file">

+

galaxy/flexbar.xml

</span>

</a>

</li>

<li class="file-stats">

<a href="#9d51a78783295e039ae9dbc298d048f0c6e01b63">

src/Flexbar.cpp

</a>

</li>

<li class="file-stats">

<a href="#b6f48f09ba51f7c4968eda298367c9dce9d126e3">

src/FlexbarIO.h

</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="#39ce06c130af5661718537ce52c57783c42daa69">

src/PairedAlign.h

</a>

</li>

<li class="file-stats">

<a href="#5892684acbf66442a550859d89842772d4e04d36">

src/PairedOutput.h

</a>

</li>

<li class="file-stats">

<a href="#62c9118c70f0995099615beb749b39099b0e417d">

src/QualTrimming.h

</a>

</li>

<li class="file-stats">

<a href="#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd">

src/SeqAlign.h

</a>

</li>

<li class="file-stats">

<a href="#66f0e3b2db8f7898f9ac09c323e12f2e1acfe23d">

src/SeqAlignPair.h

</a>

</li>

<li class="file-stats">

<a href="#aa49d3edaf982a9eb8ecad9841b1507eba6ed69a">

src/SeqInput.h

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>

<hr>

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

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

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

</tr>

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

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

2

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

2

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

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

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

<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

</td>

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

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

</td>

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

<pre style="margin: 0;">-<span id="LC5" class="line" lang="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">4</span>.0"</span> <span class="p">)</span></span>

</pre>

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

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

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="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">5</span>.0"</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

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

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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

<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: #008080;">FLEXBAR_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include <span class="p">)</span></span>

</pre>

</td>

</tr>

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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

</td>

<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

</td>

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

<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>

</td>

</tr>

</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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

1

</td>

<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"><span class="gu" style="color: #800080; font-weight: 600;">## Flexbar – flexible barcode and adapter removal</span></span>

</pre>

</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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC2" 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="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

</pre>

</td>

</tr>

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

</td>

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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. <span class="idiff left right">Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided, e.g. trimming of homopolymers at read ends. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The software supports data in fasta and fastq format from multiple sequencing platforms</span>.</span>

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

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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: #008080;">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: #008080;">Johannes Roehr</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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<pre style="margin: 0;"> <span id="LC6" 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">@@ -22,7 +22,15 @@ See article on [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/24832523)</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Download</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">Flexbar source code as well as binaries for Linux and Mac OS can be downloaded on the <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span> page. Please follow instructions for building or setup of binaries below. Additionally, Flexbar is available via package manager on Debian systems and in Conda. Versions before 2.4 can be found on the <span class="p">[</span><span class="nv" style="color: #008080;">old</span><span class="p">](</span><span class="sx" style="color: #d14;">https://sourceforge.net/projects/flexbar</span><span class="p">)</span> page.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">Flexbar source code as well as binaries for Linux and Mac OS can be downloaded on the <span class="p">[</span><span class="nv" style="color: #008080;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span> page. Please follow instructions for building or setup of binaries below. Additionally, Flexbar is available via package manager on Debian systems, in Homebrew, and in Bioconda. Versions before 2.4 can be found on the <span class="p">[</span><span class="nv" style="color: #008080;">old</span><span class="p">](</span><span class="sx" style="color: #d14;">https://sourceforge.net/projects/flexbar</span><span class="p">)</span> page.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">Installation with package managers:</span>

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

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">*</span> Debian: <span class="sb" style="color: #d14;">`sudo apt install flexbar`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">*</span> Homebrew: <span class="sb" style="color: #d14;">`brew install brewsci/science/flexbar`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> Bioconda: <span class="sb" style="color: #d14;">`conda install -c bioconda flexbar`</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">To get the latest version and best performance consider to build Flexbar from source.</span>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Building from source</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,20 +38,20 @@ 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="LC38" 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). For example on Debian systems, install the packages <span class="sb" style="color: #d14;">`libtbb-dev`</span> and <span class="sb" style="color: #d14;">`libtbb2`</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="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="p">*</span> Get SeqAn library version 2.4.0 <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">4</span> source code <span class="p">[</span><span class="nv" style="color: #008080;">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="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">5.0</span> source code <span class="p">[</span><span class="nv" style="color: #008080;">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_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<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">

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

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;">      tar xzf flexbar-3.<span class="idiff left right">4</span>.0.tar.gz</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;">      tar xzf flexbar-3.<span class="idiff left right">5</span>.0.tar.gz</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;">      tar xJf seqan-library-2.4.0.tar.xz</span></span>

</pre>

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<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">

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

</pre>

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<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">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown">Move SeqAn include folder to Flexbar:</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC42" class="line" lang="markdown"><span class="sb" style="color: #d14;">      mv seqan-library-2.4.0/include flexbar-3.<span class="idiff left right">4</span>.0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;">      mv seqan-library-2.4.0/include flexbar-3.<span class="idiff left right">5</span>.0</span></span>

</pre>

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

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

</pre>

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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="markdown">Use these commands for building:</span>

</pre>

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<td class="diff-line-num new_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="LC53" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;">      cd flexbar-3.<span class="idiff left right">4</span>.0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="markdown"><span class="sb" style="color: #d14;">      cd flexbar-3.<span class="idiff left right">5</span>.0</span></span>

</pre>

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

47

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="sb" style="color: #d14;">      cmake .</span></span>

</pre>

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48

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<td class="diff-line-num new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="sb" style="color: #d14;">      make</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="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,12 +65,12 @@ For execution of provided Flexbar binaries, the corresponding TBB library has to</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Linux</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" 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>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"><span class="sb" style="color: #d14;">      export LD_LIBRARY_PATH=/<span class="idiff left right">path/FlexbarDir</span>:$LD_LIBRARY_PATH</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="sb" style="color: #d14;">      export LD_LIBRARY_PATH=/<span class="idiff left right">YourPath/flexbar-3.5.0-linux</span>:$LD_LIBRARY_PATH</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Mac OS</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown">It applies the same as for Linux. Make the file libtbb.dylib available by setting the lib search path:</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); 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="markdown"><span class="sb" style="color: #d14;">      export DYLD_LIBRARY_PATH=/<span class="idiff left right">path/FlexbarDir</span>:$DYLD_LIBRARY_PATH</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;">      export DYLD_LIBRARY_PATH=/<span class="idiff left right">YourPath/flexbar-3.5.0-macos</span>:$DYLD_LIBRARY_PATH</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Program usage</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">@@ -95,7 +103,7 @@ To remove adapter sequences from single-end reads, specify a file with adapters</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown">For paired-end libraries, specify both files with paired reads and a fasta file with adapters for removal. Given adapters are trimmed in right mode per default. It is recommended to activate the pair overlap detection in case of standard paired reads. This increases the sensitivity by removing very short parts of adapters if an overlap is detected for a pair.</span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;">      flexbar -r r1.fq -p r2.fq -a a<span class="idiff left right">dapters</span>.fa -ap ON</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="sb" style="color: #d14;">     flexbar -r r1.fq -p r2.fq -a a<span class="idiff left right">1.fa -a2 a2</span>.fa -ap ON</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Adapter removal presets</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"></span>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">flexbar (1:3.5.0-1) unstable; urgency=medium</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debhelper-compat 12</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards-Version: 4.4.0</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Secure URI in copyright format</span>

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Sat, 27 Jul 2019 21:27:50 +0200</span>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">flexbar (1:3.4.0-2) unstable; urgency=medium</span>

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

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>

deleted

</a>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="plaintext">11</span></pre>

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</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,13 +4,13 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>

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

4

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">           Tony Travis <ajt@minke.ukfsn.org></span>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</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="plaintext">Priority: optional</span>

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

7

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>

</pre>

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

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</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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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               libtbb-dev,</span>

</pre>

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

9

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

9

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               libseqan2-dev,</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">

11

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

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               zlib1g-dev,</span>

</pre>

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

12

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

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">               libbz2-dev</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/flexbar</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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/flexbar.git</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/seqan/flexbar</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

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

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="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</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="plaintext">Upstream-Name: Flexbar</span>

</pre>

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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="plaintext">Upstream-Contact: Johannes T. Roehr <johannes.roehr@fu-berlin.de></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="plaintext">Source: https://sourceforge.net/projects/flexbar/files/</span>

</pre>

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<br>

</li>

<li id="648cfa9d8fd7911c362a25c7df65fc8d476d8734">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#648cfa9d8fd7911c362a25c7df65fc8d476d8734"><strong>galaxy/flexbar.pl</strong></a>

<hr>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Flexbar wrapper for Galaxy tool definition, version 3.5.0</span></span>

</pre>

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: Johannes Roehr</span></span>

</pre>

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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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

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

6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>

</pre>

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

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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

8

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

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

</pre>

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

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

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$format</span><span class="p">;</span></span>

</pre>

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

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@inFiles</span><span class="p">;</span></span>

</pre>

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

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

11

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@outFiles</span><span class="p">;</span></span>

</pre>

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

12

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

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

</pre>

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13

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$compression</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

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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">

14

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

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

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">..</span><span class="nv" style="color: #008080;">$#ARGV</span><span class="p">){</span></span>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$_</span><span class="p">];</span></span>

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17

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

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.(fastq\w+)$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.(fastq\w+\.gz)$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.(fastq\w+\.bz2)$/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl">          </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="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$format</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$format</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: #008080;">$1</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl">                  <span class="nb" style="color: #0086b3;">warn</span> <span class="p">"</span><span class="s2" style="color: #d14;">Read files should have the same format.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl">                  <span class="nb" style="color: #0086b3;">exit</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl">          <span class="p">}</span></span>

</pre>

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

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl">          <span class="nv" style="color: #008080;">$format</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$arg</span><span class="p">;</span></span>

</pre>

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

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

27

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl">          <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\.fastq\w+$/\.fastq/</span><span class="p">;</span></span>

</pre>

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

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

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl">          <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\.fastq\w+\.gz$/\.fastq\.gz/</span><span class="p">;</span></span>

</pre>

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

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl">          <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\.fastq\w+\.bz2$/\.fastq\.bz2/</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">

31

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl">          <span class="nv" style="color: #008080;">$compression</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">GZ</span><span class="p">"</span>  <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.fastq\.gz$/</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_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">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl">          <span class="nv" style="color: #008080;">$compression</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">BZ2</span><span class="p">"</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.fastq\.bz2$/</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC34" class="line" lang="perl">          </span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl">          <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$_</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$arg</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat_input\w\.fastq$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat_input\w\.fastq\.gz$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat_input\w\.fastq\.bz2$/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC38" class="line" lang="perl">                  <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@inFiles</span><span class="p">,</span> <span class="nv" style="color: #008080;">$arg</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl">                  <span class="nb" style="color: #0086b3;">rename</span> <span class="nv" style="color: #008080;">$file</span><span class="p">,</span> <span class="nv" style="color: #008080;">$arg</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl">          <span class="p">}</span></span>

</pre>

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

41

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC42" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@outFiles</span><span class="p">,</span> <span class="nv" style="color: #008080;">$arg</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat\.fastq$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat\.fastq\.gz$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.dat\.fastq\.bz2$/</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$barcoded</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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"><span class="nv" style="color: #008080;">$barcoded</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$#ARGV</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/barcoded$/</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$call</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span> <span class="nv" style="color: #008080;">@ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">..</span><span class="p">(</span><span class="nv" style="color: #008080;">$#ARGV</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$barcoded</span><span class="p">)];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># $call = $call ." --zip-output ". $compression if $barcoded && $compression ne "";</span></span>

</pre>

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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="perl"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"><span class="nb" style="color: #0086b3;">system</span> <span class="nv" style="color: #008080;">$call</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">exit</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

55

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

<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"></span>

</pre>

</td>

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

56

</td>

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

<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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

<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"><span class="nb" style="color: #0086b3;">unlink</span> <span class="nv" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">warn</span> <span class="p">"</span><span class="s2" style="color: #d14;">Could not unlink </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;">: $!</span><span class="p">"</span> <span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nv" style="color: #008080;">@inFiles</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

</td>

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

<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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

<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$barcoded</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl">  <span class="nv" style="color: #008080;">$format</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\.gz//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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

<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl">  <span class="nv" style="color: #008080;">$format</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\.bz2//</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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

<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$ARGV</span><span class="p">[</span><span class="nv" style="color: #008080;">$#ARGV</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">flexbarOut</span><span class="o" style="font-weight: 600;">*.</span><span class="nv" style="color: #008080;">fastq</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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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

<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$_</span><span class="p">;</span></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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

<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl">          </span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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

<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl">          <span class="sr" style="color: #009926;">s/fastq$/$format/</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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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

<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl">          <span class="c1" style="color: #998; font-style: italic;"># s/fastq\.gz$/$format/;</span></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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

<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl">          <span class="c1" style="color: #998; font-style: italic;"># s/fastq\.bz2$/$format/;</span></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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

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

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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

<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">rename</span> <span class="nv" style="color: #008080;">$file</span><span class="p">,</span> <span class="nv" style="color: #008080;">$_</span><span class="p">;</span></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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

<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

</td>

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

<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"><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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

</td>

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

<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"><span class="k" style="font-weight: 600;">else</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

</td>

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

<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span><span class="p">(</span><span class="nv" style="color: #008080;">@outFiles</span><span class="p">){</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

</td>

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

<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl">          </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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

</td>

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

<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$_</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

</td>

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

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

</td>

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

<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl">          <span class="sr" style="color: #009926;">s/\.fastq$//</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

</td>

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

<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl">          <span class="sr" style="color: #009926;">s/\.fastq\.gz$//</span><span class="p">;</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

</td>

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

<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl">          <span class="sr" style="color: #009926;">s/\.fastq\.bz2$//</span><span class="p">;</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

</td>

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

<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl">          </span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

</td>

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

<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">rename</span> <span class="nv" style="color: #008080;">$file</span><span class="p">,</span> <span class="nv" style="color: #008080;">$_</span><span class="p">;</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

</td>

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

<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

</td>

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

<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"><span class="p">}</span></span>

</pre>

</td>

</tr>

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

</td>

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

86

</td>

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

<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d33b186e083bbba7569fc40cb94aba122a125c93">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#d33b186e083bbba7569fc40cb94aba122a125c93"><strong>galaxy/flexbar.xml</strong></a>

<hr>

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

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

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</td>

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"><!-- Flexbar tool definition for Galaxy, version 3.5.0 --></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"><!-- Author: Johannes Roehr --></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml"><span class="nt" style="color: #000080;"><tool</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"flexbar"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"Flexbar"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.5.0"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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7

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

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="xml">    <span class="nt" style="color: #000080;"><description></span>- flexible barcode and adapter removal<span class="nt" style="color: #000080;"></description></span></span>

</pre>

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9

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

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="xml">   <span class="nt" style="color: #000080;"><requirements></span></span>

</pre>

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

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml">        <span class="nt" style="color: #000080;"><requirement</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"package"</span> <span class="na" style="color: #008080;">version=</span><span class="s" style="color: #d14;">"3.5.0"</span><span class="nt" style="color: #000080;">></span>flexbar<span class="nt" style="color: #000080;"></requirement></span></span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="xml">    <span class="nt" style="color: #000080;"></requirements></span></span>

</pre>

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13

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

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="xml">   <span class="nt" style="color: #000080;"><version_command></span>flexbar --versions<span class="nt" style="color: #000080;"></version_command></span></span>

</pre>

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15

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

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="xml">   <span class="nt" style="color: #000080;"><command</span> <span class="na" style="color: #008080;">detect_errors=</span><span class="s" style="color: #d14;">"aggressive"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="xml">           <span class="cp" style="color: #999; font-weight: 600;"><![CDATA[</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $reads.mode == "se":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 ln -s '$reads.rs' '$outlog'_input1.'$reads.rs.extension' &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #elif $reads.mode == "pe":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 ln -s '$reads.r1' '$outlog'_input1.'$reads.r1.extension' &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 ln -s '$reads.r2' '$outlog'_input2.'$reads.r2.extension' &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #else:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 ln -s '$reads.rc.forward' '$outlog'_input1.'$reads.rc.forward.extension' &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 ln -s '$reads.rc.reverse' '$outlog'_input2.'$reads.rc.reverse.extension' &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $cBarcodes.select == "on":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 mkdir flexbar_barcoded &&</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #if $cBarcodes.bAdvanced.cbReads.select == "yes":</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         ln -s '$cBarcodes.bAdvanced.cbReads.bReads' '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension' &&</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         '$__tool_directory__/flexbar.pl' flexbar</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         --threads \${GALAXY_SLOTS:-1}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $reads.mode == "se":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --reads '$outlog'_input1.'$reads.rs.extension'</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #elif $reads.mode == "pe":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --reads '$outlog'_input1.'$reads.r1.extension'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --reads2 '$outlog'_input2.'$reads.r2.extension'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #else:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --reads '$outlog'_input1.'$reads.rc.forward.extension'</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --reads2 '$outlog'_input2.'$reads.rc.reverse.extension'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #end if</span></span>

</pre>

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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">

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         --max-uncalled $maxUncalled</span></span>

</pre>

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

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         --min-read-length $minReadLen</span></span>

</pre>

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

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $trimEnds.select == "on":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --pre-trim-left $trimEnds.trimLeft</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --pre-trim-right $trimEnds.trimRight</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $cTrimQual.select != "off":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #if $reads.mode == "se":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rs.ext == "fastqsanger":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format sanger</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rs.ext == "fastqsolexa":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format solexa</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rs.ext == "fastqillumina":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format i1.3</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC73" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #elif $reads.mode == "pe":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.r1.ext == "fastqsanger":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format sanger</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.r1.ext == "fastqsolexa":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format solexa</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.r1.ext == "fastqillumina":</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format i1.3</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #else:</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rc.forward.ext == "fastqsanger":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format sanger</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rc.forward.ext == "fastqsolexa":</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format solexa</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #if $reads.rc.forward.ext == "fastqillumina":</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                 --qtrim-format i1.3</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                         #end if</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 #end if</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #end if</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         </span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">         #if $cTrimQual.select == "tail":</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --qtrim TAIL</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                 --qtrim-threshold $cTrimQual.trimQualTail</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cTrimQual.trimQualPostTail</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cTrimQual.select == "win":</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --qtrim WIN</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --qtrim-threshold $cTrimQual.trimQualWin</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --qtrim-win-size $cTrimQual.trimQualWinSize</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cTrimQual.trimQualPostWin</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cTrimQual.select == "bwa":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --qtrim BWA</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --qtrim-threshold $cTrimQual.trimQualBWA</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cTrimQual.trimQualPostBWA</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC115" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cBarcodes.select == "on":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --target flexbar_barcoded/flexbarOut</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.ccBarcodes.select == "file":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcodes $cBarcodes.ccBarcodes.barcodeFile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.ccBarcodes.select == "files":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcodes $cBarcodes.ccBarcodes.barcodeFile1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcodes2 $cBarcodes.ccBarcodes.barcodeFile2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --barcode-error-rate $cBarcodes.bThresh</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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

<pre style="margin: 0;">+<span id="LC129" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --barcode-trim-end $cBarcodes.bTrimEnd</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.bAdvanced.cbReads.select == "yes":</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-reads '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.bAdvanced.cbMinOverlap.select == "yes":</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-min-overlap $cBarcodes.bAdvanced.cbMinOverlap.bMinOverlap</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cBarcodes.bAdvanced.bKeep</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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

<pre style="margin: 0;">+<span id="LC140" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cBarcodes.bAdvanced.bUnassigned</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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

<pre style="margin: 0;">+<span id="LC142" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.bAdvanced.cbTailLen.select == "yes":</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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

<pre style="margin: 0;">+<span id="LC143" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-tail-length $cBarcodes.bAdvanced.cbTailLen.bTailLen</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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

<pre style="margin: 0;">+<span id="LC144" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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

<pre style="margin: 0;">+<span id="LC146" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cBarcodes.bAdvanced.cbAlignScores.select == "yes":</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-match    $cBarcodes.bAdvanced.cbAlignScores.bMatch</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-mismatch $cBarcodes.bAdvanced.cbAlignScores.bMismatch</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --barcode-gap      $cBarcodes.bAdvanced.cbAlignScores.bGap</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC150" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cAdapters.select == "on":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.ccAdapters.select == "file":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapters '$cAdapters.ccAdapters.adapterFile'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.ccAdapters.select == "files":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapters '$cAdapters.ccAdapters.adapterFile1'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapters2 '$cAdapters.ccAdapters.adapterFile2'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.ccAdapters.select == "preset":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC164" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-preset '$cAdapters.ccAdapters.adapterPreset'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC165" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.ccAdapters.select == "seq":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC167" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-seq $cAdapters.ccAdapters.adapterSeq</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --adapter-trim-end $cAdapters.aTrimEnd</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC171" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --adapter-min-overlap $cAdapters.aMinOverlap</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC172" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --adapter-error-rate $cAdapters.aThresh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC173" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.cPairOverlap.select == "on":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-pair-overlap $cAdapters.cPairOverlap.aPairOverlap</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-min-poverlap $cAdapters.cPairOverlap.aMinPoverlap</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.aAdvanced.caTailLen.select == "yes":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-tail-length $cAdapters.aAdvanced.caTailLen.aTailLen</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC183" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.aAdvanced.cRevComp.select == "on":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="184" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC184" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-revcomp ON</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC185" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                #if $cAdapters.aAdvanced.cRevComp.aRevCompEnd != "off":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC186" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                        --adapter-revcomp-end $cAdapters.aAdvanced.cRevComp.aRevCompEnd</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC187" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.aAdvanced.cRevComp.select == "only":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-revcomp ONLY</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAdapters.aAdvanced.aReadSet</span></span>

</pre>

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

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

</tr>

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

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --adapter-cycles $cAdapters.aAdvanced.aCycles</span></span>

</pre>

</td>

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

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAdapters.aAdvanced.caAlignScores.select == "yes":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-match    $cAdapters.aAdvanced.caAlignScores.aMatch</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

199

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch</span></span>

</pre>

</td>

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

200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --adapter-gap      $cAdapters.aAdvanced.caAlignScores.aGap</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

201

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

202

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

203

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

204

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

</td>

</tr>

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

205

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $hTrim.select == "on":</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

206

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $hTrim.hTrimLeft != "":</span></span>

</pre>

</td>

</tr>

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

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --htrim-left $hTrim.hTrimLeft</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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</td>

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

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $hTrim.hTrimRight != "":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --htrim-right $hTrim.hTrimRight</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC213" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --htrim-min-length $hTrim.hMinLength</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --htrim-error-rate $hTrim.hErrorRate</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

216

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $hTrim.hAdvanced.hMinLength2 != "":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --htrim-min-length2 $hTrim.hAdvanced.hMinLength2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;">+<span id="LC219" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $hTrim.hAdvanced.hMaxLength != "":</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --htrim-max-length $hTrim.hAdvanced.hMaxLength</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $hTrim.hAdvanced.hMaxFirst</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="224" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC224" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $hTrim.hAdvanced.hTrimAdapter</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cTrimLen.select == "on":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        --post-trim-length $cTrimLen.trimLen</span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC230" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cAddOptions.select == "show":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAddOptions.logLevel</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC234" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAddOptions.numTags</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAddOptions.remTags</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAddOptions.rndTags</span></span>

</pre>

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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="xml"><span class="cp" style="color: #999; font-weight: 600;">                        $cAddOptions.singleReadsP</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        </span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC239" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $cAddOptions.cReadBundle.select == "show":</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC240" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --bundle $cAddOptions.cReadBundle.bundle</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                </span></span>

</pre>

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<td class="diff-line-num new new_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">

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                #if $cAddOptions.cReadBundle.bundles != "":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                        --bundles $cAddOptions.cReadBundle.bundles</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                #end if</span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC246" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC248" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cBarcodes.select == "off":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC249" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #if $reads.mode == "se":</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC250" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --output-reads '$rsout'.'$reads.rs.extension'</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">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #elif $reads.mode == "pe":</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --output-reads '$r1out'.'$reads.r1.extension'</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --output-reads2 '$r2out'.'$reads.r2.extension'</span></span>

</pre>

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<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="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #else:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --output-reads '$rcout.forward'.'$reads.rc.forward.extension'</span></span>

</pre>

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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="xml"><span class="cp" style="color: #999; font-weight: 600;">                                --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        #end if</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                --output-log '$outlog'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                #if $cBarcodes.select == "on":</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                        flexbar_barcoded</span></span>

</pre>

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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="xml"><span class="cp" style="color: #999; font-weight: 600;">                #end if</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;">                ]]></span></span>

</pre>

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267

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="xml">  <span class="nt" style="color: #000080;"></command></span></span>

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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

268

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="xml">  </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="xml">  </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">

270

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="xml">  <span class="nt" style="color: #000080;"><inputs></span></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">

271

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="xml">          </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">

272

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"reads"</span><span class="nt" style="color: #000080;">></span></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">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"mode"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Sequencing reads"</span><span class="nt" style="color: #000080;">></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="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"se"</span><span class="nt" style="color: #000080;">></span>Single read file<span class="nt" style="color: #000080;"></option></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">

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"pe"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Paired read files<span class="nt" style="color: #000080;"></option></span></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">

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"pc"</span><span class="nt" style="color: #000080;">></span>Paired read collection<span class="nt" style="color: #000080;"></option></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="xml">                  <span class="nt" style="color: #000080;"></param></span></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="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"se"</span><span class="nt" style="color: #000080;">></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="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rs"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fastq read file"</span><span class="nt" style="color: #000080;">/></span></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="xml">                  <span class="nt" style="color: #000080;"></when></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="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"pe"</span><span class="nt" style="color: #000080;">></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">

282

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"r1"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fastq read file 1"</span><span class="nt" style="color: #000080;">/></span></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="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"r2"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fastq read file 2"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"pc"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rc"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data_collection"</span> <span class="na" style="color: #008080;">collection_type=</span><span class="s" style="color: #d14;">"paired"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fastq pair collection"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="xml">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="xml">          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"maxUncalled"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0"</span>  <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"1) Maximum uncalled bases"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="xml">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimEnds"</span><span class="nt" style="color: #000080;">></span></span>

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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">

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"2) Trimming of read ends"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimLeft"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Left"</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimRight"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Right"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"trims specified number of bases at ends"</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC304" class="line" lang="xml">          </span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cTrimQual"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC306" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"3) Quality-based trimming"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

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

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"tail"</span><span class="nt" style="color: #000080;">></span>Tail<span class="nt" style="color: #000080;"></option></span></span>

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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC309" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"win"</span><span class="nt" style="color: #000080;">></span>Window<span class="nt" style="color: #000080;"></option></span></span>

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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"bwa"</span><span class="nt" style="color: #000080;">></span>BWA<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC313" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"tail"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC315" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualTail"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Quality threshold"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"trim right end until specified quality or higher"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="xml">                          </span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualPostTail"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"After adapter removal"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

318

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

319

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--qtrim-post-removal"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

320

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

321

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

322

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"win"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

323

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualWin"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Quality threshold"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

324

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualWinSize"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"5"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Window length"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"sliding window average quality approach from left end"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

325

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

326

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualPostWin"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"After adapter removal"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

327

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

328

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--qtrim-post-removal"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

329

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC330" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC331" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"bwa"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

332

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualBWA"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Quality threshold"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"trimming approach used by BWA"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

333

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC334" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimQualPostBWA"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"After adapter removal"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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335

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

336

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--qtrim-post-removal"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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337

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC340" class="line" lang="xml">          </span>

</pre>

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC342" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cBarcodes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC343" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"4) Barcode detection"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="346" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC346" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC347" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"ccBarcodes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Barcodes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"file"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Barcode file<span class="nt" style="color: #000080;"></option></span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"files"</span><span class="nt" style="color: #000080;">></span>Two barcode files<span class="nt" style="color: #000080;"></option></span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"file"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"barcodeFile"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta file with barcodes for reads 1"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"files"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"barcodeFile1"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta file with barcodes for reads 1"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"barcodeFile2"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta file with barcodes for reads 2"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></conditional></span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="xml">                          </span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bThresh"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0.0"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Error rate"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"allowed fraction of mismatches and indels"</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="xml">                          </span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bTrimEnd"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Trim-end mode"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LTAIL"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Left tail<span class="nt" style="color: #000080;"></option></span></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LEFT"</span><span class="nt" style="color: #000080;">></span>Left<span class="nt" style="color: #000080;"></option></span></span>

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<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">

369

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RTAIL"</span><span class="nt" style="color: #000080;">></span>Right tail<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<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">

370

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

<pre style="margin: 0;">+<span id="LC370" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RIGHT"</span><span class="nt" style="color: #000080;">></span>Right<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<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">

371

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

<pre style="margin: 0;">+<span id="LC371" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"ANY"</span><span class="nt" style="color: #000080;">></span>Any<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<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">

372

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

373

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

374

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

<pre style="margin: 0;">+<span id="LC374" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><section</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bAdvanced"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"Advanced options"</span> <span class="na" style="color: #008080;">expanded=</span><span class="s" style="color: #d14;">"false"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

375

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="xml">                                  </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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

<pre style="margin: 0;">+<span id="LC376" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cbReads"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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

<pre style="margin: 0;">+<span id="LC377" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Separate barcode reads"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

378

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

<pre style="margin: 0;">+<span id="LC378" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

379

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

<pre style="margin: 0;">+<span id="LC379" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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

<pre style="margin: 0;">+<span id="LC381" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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

<pre style="margin: 0;">+<span id="LC383" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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

<pre style="margin: 0;">+<span id="LC384" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bReads"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fastq file with separate barcode reads"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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

<pre style="margin: 0;">+<span id="LC385" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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

<pre style="margin: 0;">+<span id="LC386" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

387

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

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cbMinOverlap"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Change minimum overlap"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"default: barcode length"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

390

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

<pre style="margin: 0;">+<span id="LC390" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

391

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

<pre style="margin: 0;">+<span id="LC391" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

392

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

393

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

394

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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

<pre style="margin: 0;">+<span id="LC395" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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

<pre style="margin: 0;">+<span id="LC396" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bMinOverlap"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum overlap"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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

<pre style="margin: 0;">+<span id="LC398" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

399

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

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

<pre style="margin: 0;">+<span id="LC400" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bKeep"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Remove barcodes within reads"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

</td>

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

<pre style="margin: 0;">+<span id="LC401" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

</td>

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

<pre style="margin: 0;">+<span id="LC402" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--barcode-keep"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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

<pre style="margin: 0;">+<span id="LC403" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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

<pre style="margin: 0;">+<span id="LC404" class="line" lang="xml">                                  </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bUnassigned"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Include unassigned reads"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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

<pre style="margin: 0;">+<span id="LC406" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--barcode-unassigned"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

410

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cbTailLen"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Change tail length"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

412

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

<pre style="margin: 0;">+<span id="LC412" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

413

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

<pre style="margin: 0;">+<span id="LC413" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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

<pre style="margin: 0;">+<span id="LC414" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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

<pre style="margin: 0;">+<span id="LC415" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

416

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

<pre style="margin: 0;">+<span id="LC416" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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

<pre style="margin: 0;">+<span id="LC417" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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

<pre style="margin: 0;">+<span id="LC418" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bTailLen"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Tail length"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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

<pre style="margin: 0;">+<span id="LC419" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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

<pre style="margin: 0;">+<span id="LC420" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC422" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cbAlignScores"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Modify alignment scores"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

424

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

426

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

427

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

428

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

429

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

430

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bMatch"</span>    <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"1"</span>  <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Match"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

431

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bMismatch"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"-1"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Mismatch"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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432

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bGap"</span>      <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"-9"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Gap"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></section></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="xml">          </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC439" class="line" lang="xml">          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cAdapters"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"5) Adapter removal"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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442

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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444

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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448

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"ccAdapters"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Adapter source"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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450

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"file"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Adapter file<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"files"</span><span class="nt" style="color: #000080;">></span>Two adapter files<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"preset"</span><span class="nt" style="color: #000080;">></span>Illumina preset<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"seq"</span><span class="nt" style="color: #000080;">></span>Single sequence<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"file"</span><span class="nt" style="color: #000080;">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"adapterFile"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta adapter file"</span><span class="nt" style="color: #000080;">/></span></span>

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<td class="diff-line-num new new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"files"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

459

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

<pre style="margin: 0;">+<span id="LC459" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"adapterFile1"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta adapter file for reads 1"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

460

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

<pre style="margin: 0;">+<span id="LC460" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"fasta"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"adapterFile2"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"data"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Fasta adapter file for reads 2"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

461

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

462

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

<pre style="margin: 0;">+<span id="LC462" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"preset"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

463

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

<pre style="margin: 0;">+<span id="LC463" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"adapterPreset"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Adapter preset"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

464

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

<pre style="margin: 0;">+<span id="LC464" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"TruSeq"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>TruSeq LT and HT-based kits<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

465

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

<pre style="margin: 0;">+<span id="LC465" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"SmallRNA"</span><span class="nt" style="color: #000080;">></span>TruSeq Small RNA<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

466

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"Methyl"</span><span class="nt" style="color: #000080;">></span>TruSeq DNA Methylation and ScriptSeq<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

467

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

<pre style="margin: 0;">+<span id="LC467" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"Ribo"</span><span class="nt" style="color: #000080;">></span>TruSeq Ribo Profile<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

468

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

<pre style="margin: 0;">+<span id="LC468" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"Nextera"</span><span class="nt" style="color: #000080;">></span>Nextera, AmpliSeq, and TruSight<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

469

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

<pre style="margin: 0;">+<span id="LC469" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"NexteraMP"</span><span class="nt" style="color: #000080;">></span>Nextera Mate Pair<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

470

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

472

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"seq"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"adapterSeq"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"40"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Adapter sequence"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

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<td class="diff-line-num new new_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="xml">                          </span>

</pre>

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

477

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aMinOverlap"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum overlap"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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

478

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aThresh"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0.1"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Error rate"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"allowed fraction of mismatches and indels"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC480" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aTrimEnd"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Trim-end mode"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

481

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RIGHT"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Right<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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482

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LEFT"</span><span class="nt" style="color: #000080;">></span>Left<span class="nt" style="color: #000080;"></option></span></span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RTAIL"</span><span class="nt" style="color: #000080;">></span>Right tail<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC484" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LTAIL"</span><span class="nt" style="color: #000080;">></span>Left tail<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC485" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"ANY"</span><span class="nt" style="color: #000080;">></span>Any<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC488" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cPairOverlap"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

489

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

<pre style="margin: 0;">+<span id="LC489" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Pair overlap detection"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aPairOverlap"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Detection mode"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"ON"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Standard<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"SHORT"</span><span class="nt" style="color: #000080;">></span>Trim short<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aMinPoverlap"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"40"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum pair overlap"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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

<pre style="margin: 0;">+<span id="LC504" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><section</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aAdvanced"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"Advanced options"</span> <span class="na" style="color: #008080;">expanded=</span><span class="s" style="color: #d14;">"false"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

506

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"caTailLen"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Change tail length"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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

<pre style="margin: 0;">+<span id="LC509" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

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

510

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

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

511

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

513

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

<pre style="margin: 0;">+<span id="LC513" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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

<pre style="margin: 0;">+<span id="LC514" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aTailLen"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Tail length"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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</td>

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

516

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

<pre style="margin: 0;">+<span id="LC516" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

517

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

518

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

<pre style="margin: 0;">+<span id="LC518" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cRevComp"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

519

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

<pre style="margin: 0;">+<span id="LC519" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Reverse complements of adapters"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

520

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

<pre style="margin: 0;">+<span id="LC520" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

521

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

<pre style="margin: 0;">+<span id="LC521" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

522

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

<pre style="margin: 0;">+<span id="LC522" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"only"</span><span class="nt" style="color: #000080;">></span>Only<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

523

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

<pre style="margin: 0;">+<span id="LC523" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

524

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

<pre style="margin: 0;">+<span id="LC524" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

525

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

526

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

527

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

<pre style="margin: 0;">+<span id="LC527" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aRevCompEnd"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Different trim-end for reverse complements"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

528

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

<pre style="margin: 0;">+<span id="LC528" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

529

</td>

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

<pre style="margin: 0;">+<span id="LC529" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RIGHT"</span><span class="nt" style="color: #000080;">></span>Right<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

530

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

<pre style="margin: 0;">+<span id="LC530" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LEFT"</span><span class="nt" style="color: #000080;">></span>Left<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

531

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

<pre style="margin: 0;">+<span id="LC531" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"RTAIL"</span><span class="nt" style="color: #000080;">></span>Right tail<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

532

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

<pre style="margin: 0;">+<span id="LC532" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"LTAIL"</span><span class="nt" style="color: #000080;">></span>Left tail<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

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

<pre style="margin: 0;">+<span id="LC533" class="line" lang="xml">                                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"ANY"</span><span class="nt" style="color: #000080;">></span>Any<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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

<pre style="margin: 0;">+<span id="LC534" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

535

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

<pre style="margin: 0;">+<span id="LC535" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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

536

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

<pre style="margin: 0;">+<span id="LC536" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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</td>

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

537

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

<pre style="margin: 0;">+<span id="LC537" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

538

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

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

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

539

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

<pre style="margin: 0;">+<span id="LC539" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aReadSet"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Removal for single read set"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

</td>

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

<pre style="margin: 0;">+<span id="LC540" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

541

</td>

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

<pre style="margin: 0;">+<span id="LC541" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--adapter-read-set 1"</span><span class="nt" style="color: #000080;">></span>1st<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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

<pre style="margin: 0;">+<span id="LC542" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--adapter-read-set 2"</span><span class="nt" style="color: #000080;">></span>2nd<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aCycles"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Number of removal cycles"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"caAlignScores"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

548

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Modify alignment scores"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

549

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>No<span class="nt" style="color: #000080;"></option></span></span>

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550

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span>Yes<span class="nt" style="color: #000080;"></option></span></span>

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<td class="diff-line-num new new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></param></span></span>

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552

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"no"</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"yes"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

555

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aMatch"</span>    <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"1"</span>  <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Match"</span><span class="nt" style="color: #000080;">/></span></span>

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<td class="diff-line-num new new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC556" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aMismatch"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"-1"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Mismatch"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

557

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="xml">                                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"aGap"</span>      <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"-6"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Gap"</span><span class="nt" style="color: #000080;">/></span></span>

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC559" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></section></span></span>

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561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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562

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="xml">          </span>

</pre>

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564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="xml">          </span>

</pre>

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

565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hTrim"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"6) Trimming of homopolymers"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_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">

567

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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568

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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570

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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571

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hTrimLeft"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Trim homopolymers on left end"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC574" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hTrimRight"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Trim homopolymers on right end"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"true"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"for example AT"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="xml">                          </span>

</pre>

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hMinLength"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"3"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum length"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hErrorRate"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"float"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"0.1"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Error rate"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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</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

</td>

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

<pre style="margin: 0;">+<span id="LC578" class="line" lang="xml">                          </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC579" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><section</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hAdvanced"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"Advanced options"</span> <span class="na" style="color: #008080;">expanded=</span><span class="s" style="color: #d14;">"false"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC580" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC581" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hMaxLength"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Maximum length"</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

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

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

<pre style="margin: 0;">+<span id="LC583" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hMaxFirst"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Maximum length only for first one"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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

</td>

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

<pre style="margin: 0;">+<span id="LC584" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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

</td>

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

<pre style="margin: 0;">+<span id="LC585" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--htrim-max-first"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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

586

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

<pre style="margin: 0;">+<span id="LC586" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

587

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

<pre style="margin: 0;">+<span id="LC587" class="line" lang="xml">                                  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

</td>

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

<pre style="margin: 0;">+<span id="LC588" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hMinLength2"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Minimum length after first one"</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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

<pre style="margin: 0;">+<span id="LC589" class="line" lang="xml">                                  </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

590

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

<pre style="margin: 0;">+<span id="LC590" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"hTrimAdapter"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Only in case of adapter on same side"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

</td>

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

<pre style="margin: 0;">+<span id="LC591" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

</td>

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

<pre style="margin: 0;">+<span id="LC592" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--htrim-adapter"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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

<pre style="margin: 0;">+<span id="LC593" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></section></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

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

<pre style="margin: 0;">+<span id="LC597" class="line" lang="xml">          </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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

<pre style="margin: 0;">+<span id="LC598" class="line" lang="xml">          </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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

<pre style="margin: 0;">+<span id="LC599" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cTrimLen"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

600

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

<pre style="margin: 0;">+<span id="LC600" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"7) Trimming to length"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

601

</td>

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

<pre style="margin: 0;">+<span id="LC601" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

</td>

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

<pre style="margin: 0;">+<span id="LC602" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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

<pre style="margin: 0;">+<span id="LC603" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

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

<pre style="margin: 0;">+<span id="LC604" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"off"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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

<pre style="margin: 0;">+<span id="LC605" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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

606

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

<pre style="margin: 0;">+<span id="LC606" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"on"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

</td>

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

<pre style="margin: 0;">+<span id="LC607" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"trimLen"</span> <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Length"</span> <span class="na" style="color: #008080;">help=</span><span class="s" style="color: #d14;">"trim reads to certain length from right"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

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

<pre style="margin: 0;">+<span id="LC608" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

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

<pre style="margin: 0;">+<span id="LC609" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

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

<pre style="margin: 0;">+<span id="LC610" class="line" lang="xml">          </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

611

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

<pre style="margin: 0;">+<span id="LC611" class="line" lang="xml">          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"minReadLen"</span>  <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"20"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"8) Minimum read length"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

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

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

613

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

<pre style="margin: 0;">+<span id="LC613" class="line" lang="xml">          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cAddOptions"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

</td>

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

<pre style="margin: 0;">+<span id="LC614" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Additional options"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

615

</td>

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

<pre style="margin: 0;">+<span id="LC615" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"hide"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Hide<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

616

</td>

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

<pre style="margin: 0;">+<span id="LC616" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"show"</span><span class="nt" style="color: #000080;">></span>Show<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

617

</td>

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

<pre style="margin: 0;">+<span id="LC617" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></param></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

618

</td>

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

<pre style="margin: 0;">+<span id="LC618" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"hide"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

</td>

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

<pre style="margin: 0;">+<span id="LC619" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

620

</td>

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

<pre style="margin: 0;">+<span id="LC620" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"show"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

</td>

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

621

</td>

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

<pre style="margin: 0;">+<span id="LC621" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"logLevel"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Alignment logging"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

</td>

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

<pre style="margin: 0;">+<span id="LC622" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

623

</td>

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

<pre style="margin: 0;">+<span id="LC623" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--align-log ALL"</span><span class="nt" style="color: #000080;">></span>All<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

624

</td>

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

<pre style="margin: 0;">+<span id="LC624" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--align-log MOD"</span><span class="nt" style="color: #000080;">></span>Modified<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

</td>

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

<pre style="margin: 0;">+<span id="LC625" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--align-log TAB"</span><span class="nt" style="color: #000080;">></span>Tabular<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

626

</td>

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

<pre style="margin: 0;">+<span id="LC626" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

</td>

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

<pre style="margin: 0;">+<span id="LC627" class="line" lang="xml">                          </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

</td>

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

<pre style="margin: 0;">+<span id="LC628" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"numTags"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Number tags"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

</td>

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

<pre style="margin: 0;">+<span id="LC629" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

</td>

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

<pre style="margin: 0;">+<span id="LC630" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--number-tags"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

631

</td>

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

<pre style="margin: 0;">+<span id="LC631" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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

<pre style="margin: 0;">+<span id="LC632" class="line" lang="xml">                          </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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

<pre style="margin: 0;">+<span id="LC633" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"remTags"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Removal tags"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

</td>

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

<pre style="margin: 0;">+<span id="LC634" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

</td>

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

<pre style="margin: 0;">+<span id="LC635" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--removal-tags"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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

<pre style="margin: 0;">+<span id="LC636" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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

<pre style="margin: 0;">+<span id="LC637" class="line" lang="xml">                          </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

638

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

<pre style="margin: 0;">+<span id="LC638" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rndTags"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"UMI tags"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

639

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

<pre style="margin: 0;">+<span id="LC639" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

640

</td>

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

<pre style="margin: 0;">+<span id="LC640" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--umi-tags"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

641

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

<pre style="margin: 0;">+<span id="LC641" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

642

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

<pre style="margin: 0;">+<span id="LC642" class="line" lang="xml">                          </span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

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

<pre style="margin: 0;">+<span id="LC643" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"singleReadsP"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Single reads as paired"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

644

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

<pre style="margin: 0;">+<span id="LC644" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Off<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

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

<pre style="margin: 0;">+<span id="LC645" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"--single-reads-paired"</span><span class="nt" style="color: #000080;">></span>On<span class="nt" style="color: #000080;"></option></span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

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

<pre style="margin: 0;">+<span id="LC646" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></param></span></span>

</pre>

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647

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="xml">                          </span>

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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

648

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="xml">                          <span class="nt" style="color: #000080;"><conditional</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cReadBundle"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

649

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"select"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Read bundle options"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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650

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"hide"</span> <span class="na" style="color: #008080;">selected=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">></span>Hide<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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651

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"show"</span><span class="nt" style="color: #000080;">></span>Show<span class="nt" style="color: #000080;"></option></span></span>

</pre>

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652

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></param></span></span>

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653

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"hide"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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654

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

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655

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"><when</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"show"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

656

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bundle"</span>  <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"256"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Number of paired reads per bundle"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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657

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="xml">                                          <span class="nt" style="color: #000080;"><param</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"bundles"</span>  <span class="na" style="color: #008080;">size=</span><span class="s" style="color: #d14;">"4"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">""</span> <span class="na" style="color: #008080;">optional=</span><span class="s" style="color: #d14;">"true"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Only certain number of bundles for testing"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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658

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="xml">                                  <span class="nt" style="color: #000080;"></when></span></span>

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="xml">                          <span class="nt" style="color: #000080;"></conditional></span></span>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="xml">                  <span class="nt" style="color: #000080;"></when></span></span>

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661

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="xml">          <span class="nt" style="color: #000080;"></conditional></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="xml">          </span>

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663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="xml">          <span class="nt" style="color: #000080;"></inputs></span></span>

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="xml">  </span>

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<td class="diff-line-num new new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

</td>

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

<pre style="margin: 0;">+<span id="LC665" class="line" lang="xml">  <span class="nt" style="color: #000080;"><outputs></span></span>

</pre>

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</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

666

</td>

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

<pre style="margin: 0;">+<span id="LC666" class="line" lang="xml">      <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"outlog"</span> <span class="na" style="color: #008080;">format=</span><span class="s" style="color: #d14;">"txt"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar log for ${on_string}"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

667

</td>

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

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

668

</td>

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

<pre style="margin: 0;">+<span id="LC668" class="line" lang="xml">          <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rsout"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${reads.rs.name}"</span> <span class="na" style="color: #008080;">format_source=</span><span class="s" style="color: #d14;">"rs"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

</td>

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

<pre style="margin: 0;">+<span id="LC669" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>reads['mode'] == 'se'<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

670

</td>

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

<pre style="margin: 0;">+<span id="LC670" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>cBarcodes['select'] == "off"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

671

</td>

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

<pre style="margin: 0;">+<span id="LC671" class="line" lang="xml">          <span class="nt" style="color: #000080;"></data></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

</td>

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

<pre style="margin: 0;">+<span id="LC672" class="line" lang="xml">          </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

</td>

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

<pre style="margin: 0;">+<span id="LC673" class="line" lang="xml">          <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"r1out"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${reads.r1.name}"</span> <span class="na" style="color: #008080;">format_source=</span><span class="s" style="color: #d14;">"r1"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

</td>

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

<pre style="margin: 0;">+<span id="LC674" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>reads['mode'] == "pe"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

675

</td>

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

<pre style="margin: 0;">+<span id="LC675" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>cBarcodes['select'] == "off"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

676

</td>

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

<pre style="margin: 0;">+<span id="LC676" class="line" lang="xml">          <span class="nt" style="color: #000080;"></data></span></span>

</pre>

</td>

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

677

</td>

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

<pre style="margin: 0;">+<span id="LC677" class="line" lang="xml">          <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"r2out"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${reads.r2.name}"</span> <span class="na" style="color: #008080;">format_source=</span><span class="s" style="color: #d14;">"r2"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

</td>

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

678

</td>

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

<pre style="margin: 0;">+<span id="LC678" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>reads['mode'] == "pe"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

679

</td>

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

<pre style="margin: 0;">+<span id="LC679" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>cBarcodes['select'] == "off"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

680

</td>

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

<pre style="margin: 0;">+<span id="LC680" class="line" lang="xml">          <span class="nt" style="color: #000080;"></data></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

681

</td>

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

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

682

</td>

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

<pre style="margin: 0;">+<span id="LC682" class="line" lang="xml">          <span class="nt" style="color: #000080;"><collection</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"rcout"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"paired"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${on_string}"</span><span class="nt" style="color: #000080;">></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

683

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>reads['mode'] == "pc"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

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684

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>cBarcodes['select'] == "off"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"forward"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${reads.rc.forward.name}"</span> <span class="na" style="color: #008080;">format_source=</span><span class="s" style="color: #d14;">"rc['forward']"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

686

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><data</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"reverse"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${reads.rc.reverse.name}"</span> <span class="na" style="color: #008080;">format_source=</span><span class="s" style="color: #d14;">"rc['reverse']"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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687

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="xml">          <span class="nt" style="color: #000080;"></collection></span></span>

</pre>

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688

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="xml">          </span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="xml">          <span class="nt" style="color: #000080;"><collection</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"list"</span> <span class="na" style="color: #008080;">label=</span><span class="s" style="color: #d14;">"Flexbar on ${on_string}"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"barcoded"</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><filter></span>cBarcodes['select'] == "on"<span class="nt" style="color: #000080;"></filter></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="xml">                  <span class="nt" style="color: #000080;"><discover_datasets</span> <span class="na" style="color: #008080;">pattern=</span><span class="s" style="color: #d14;">"__designation_and_ext__"</span> <span class="na" style="color: #008080;">directory=</span><span class="s" style="color: #d14;">"flexbar_barcoded"</span> <span class="na" style="color: #008080;">visible=</span><span class="s" style="color: #d14;">"true"</span><span class="nt" style="color: #000080;">/></span></span>

</pre>

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692

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="xml">          <span class="nt" style="color: #000080;"></collection></span></span>

</pre>

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693

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="xml">          </span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="xml">  <span class="nt" style="color: #000080;"></outputs></span></span>

</pre>

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695

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="xml">  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="xml">  <span class="nt" style="color: #000080;"><help></span></span>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="xml"></span>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="xml">**Description**</span>

</pre>

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699

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="xml"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="xml">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. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fastq format, e.g. from the Illumina platform. Flexbar is available on the project_ page.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="xml"></span>

</pre>

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</td>

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="xml">.. _project: https://github.com/seqan/flexbar</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

703

</td>

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

<pre style="margin: 0;">+<span id="LC703" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

704

</td>

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

<pre style="margin: 0;">+<span id="LC704" class="line" lang="xml">------</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

705

</td>

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

<pre style="margin: 0;">+<span id="LC705" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

706

</td>

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

<pre style="margin: 0;">+<span id="LC706" class="line" lang="xml">**Trim-end modes**</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

</td>

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

<pre style="margin: 0;">+<span id="LC707" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

</td>

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

<pre style="margin: 0;">+<span id="LC708" class="line" lang="xml">**Any:** longer side of read remains after overlap removal</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

</td>

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

<pre style="margin: 0;">+<span id="LC709" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

</td>

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

<pre style="margin: 0;">+<span id="LC710" class="line" lang="xml">**Left:** right side remains after removal, align before or at read end</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

</td>

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

<pre style="margin: 0;">+<span id="LC711" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

</td>

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

<pre style="margin: 0;">+<span id="LC712" class="line" lang="xml">**Right:** left part remains after removal, align after or at read start</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

</td>

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

<pre style="margin: 0;">+<span id="LC713" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

714

</td>

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

<pre style="margin: 0;">+<span id="LC714" class="line" lang="xml">**Left tail:** consider first n bases of reads in alignment</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

</td>

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

<pre style="margin: 0;">+<span id="LC715" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

716

</td>

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

<pre style="margin: 0;">+<span id="LC716" class="line" lang="xml">**Right tail:** use only last n bases, see tail-length options</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

717

</td>

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

<pre style="margin: 0;">+<span id="LC717" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

</td>

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

<pre style="margin: 0;">+<span id="LC718" class="line" lang="xml">------</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

</td>

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

<pre style="margin: 0;">+<span id="LC719" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

720

</td>

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

<pre style="margin: 0;">+<span id="LC720" class="line" lang="xml">**Documentation**</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

</td>

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

<pre style="margin: 0;">+<span id="LC721" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

</td>

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

<pre style="margin: 0;">+<span id="LC722" class="line" lang="xml">Further documentation is available on the `manual`__ page and via the command line help screen.</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

</td>

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

<pre style="margin: 0;">+<span id="LC723" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

</td>

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

<pre style="margin: 0;">+<span id="LC724" class="line" lang="xml">.. __: https://github.com/seqan/flexbar/wiki</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

</td>

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

<pre style="margin: 0;">+<span id="LC725" class="line" lang="xml"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

726

</td>

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

<pre style="margin: 0;">+<span id="LC726" class="line" lang="xml">------</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

727

</td>

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

<pre style="margin: 0;">+<span id="LC727" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

728

</td>

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

<pre style="margin: 0;">+<span id="LC728" class="line" lang="xml">**References**</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

729

</td>

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

<pre style="margin: 0;">+<span id="LC729" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

</td>

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

<pre style="margin: 0;">+<span id="LC730" class="line" lang="xml">Johannes T. Roehr, Christoph Dieterich, Knut Reinert:  </span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

</td>

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

<pre style="margin: 0;">+<span id="LC731" class="line" lang="xml">Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

732

</td>

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

<pre style="margin: 0;">+<span id="LC732" class="line" lang="xml"></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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

733

</td>

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

<pre style="margin: 0;">+<span id="LC733" class="line" lang="xml">Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:  </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

734

</td>

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

<pre style="margin: 0;">+<span id="LC734" class="line" lang="xml">Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

</td>

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

<pre style="margin: 0;">+<span id="LC735" class="line" lang="xml"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

</td>

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

<pre style="margin: 0;">+<span id="LC736" class="line" lang="xml">  <span class="nt" style="color: #000080;"></help></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

</td>

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

<pre style="margin: 0;">+<span id="LC737" class="line" lang="xml"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

</td>

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

<pre style="margin: 0;">+<span id="LC738" class="line" lang="xml"><span class="nt" style="color: #000080;"></tool></span></span>

</pre>

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

739

</td>

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

<pre style="margin: 0;">+<span id="LC739" class="line" lang="xml"></span></pre>

</td>

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<br>

</li>

<li id="9d51a78783295e039ae9dbc298d048f0c6e01b63">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#9d51a78783295e039ae9dbc298d048f0c6e01b63"><strong>src/Flexbar.cpp</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">@@ -2,7 +2,7 @@</td>

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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="cpp"><span class="cm" style="color: #998; font-style: italic;">   </span></span>

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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="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" 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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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">4</span>.0</span></span>

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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">5</span>.0</span></span>

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<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 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;">   BSD 3-Clause License</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">

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8

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,8 +29,8 @@ int main(int argc, const char* argv[]){</td>

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<pre style="margin: 0;"> <span id="LC29" 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="LC30" 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="LC31" class="line" lang="cpp">   </span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">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">4</span>.0"</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC33" 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">June 2018</span>"</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC32" 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">5</span>.0"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC33" 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 2019</span>"</span><span class="p">;</span></span>

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

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC35" 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="LC36" class="line" lang="cpp">   </span>

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<br>

</li>

<li id="b6f48f09ba51f7c4968eda298367c9dce9d126e3">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#b6f48f09ba51f7c4968eda298367c9dce9d126e3"><strong>src/FlexbarIO.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -295,8 +295,7 @@ void checkInputType(const std::string path, flexbar::FileFormat &format, const b</td>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c">            <span class="n" style="color: #333;">try</span><span class="p">{</span></span>

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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="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">atEnd</span><span class="p">(</span><span class="n" style="color: #333;">seqFileIn</span><span class="p">)){</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c">                            </span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c">                            <span class="n" style="color: #333;">FSeqStr</span> <span class="n" style="color: #333;">seq</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;">FString</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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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c">                            <span class="n" style="color: #333;">FString</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c">                            </span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c">                            <span class="n" style="color: #333;">readRecord</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c">                            </span>

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<br>

</li>

<li id="e46cbf6df1dcc17df0ea6052697f523aefb88ff4">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#e46cbf6df1dcc17df0ea6052697f523aefb88ff4"><strong>src/FlexbarTypes.h</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">@@ -11,14 +11,15 @@ class SeqRead {</td>

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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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<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 class="n" style="color: #333;">umi</span><span class="p">;</span></span>

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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;">bool</span> <span class="n" style="color: #333;">rmAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">rmAdapterRC</span><span class="p">,</span> <span class="n" style="color: #333;">pairOverlap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">rmAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">rmAdapterRC</span><span class="p">,</span> <span class="n" style="color: #333;">pairOverlap</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">poRemoval</span></span><span class="p">;</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="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>

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<pre style="margin: 0;"> <span id="LC17" 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>

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<pre style="margin: 0;"> <span id="LC18" 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>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">             <span class="n" style="color: #333;">rmAdapter</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c">             <span class="n" style="color: #333;">rmAdapterRC</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c">             <span class="n" style="color: #333;">pairOverlap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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="21" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC21" class="line" lang="c">             <span class="n" style="color: #333;">pairOverlap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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="22" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC22" class="line" lang="c">             <span class="n" style="color: #333;">poRemoval</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_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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<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="p">}</span></span>

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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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c">     </span>

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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="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="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>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +28,8 @@ class SeqRead {</td>

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

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<pre style="margin: 0;"> <span id="LC28" 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>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">             <span class="n" style="color: #333;">rmAdapter</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">             <span class="n" style="color: #333;">rmAdapterRC</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="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="LC30" class="line" lang="c">             <span class="n" style="color: #333;">pairOverlap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<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="c">             <span class="n" style="color: #333;">pairOverlap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC32" class="line" lang="c">             <span class="n" style="color: #333;">poRemoval</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">){</span></span>

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<td class="diff-line-num 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="c">     <span class="p">}</span></span>

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

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<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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,6 +235,12 @@ namespace flexbar{</td>

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

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c">            <span class="n" style="color: #333;">AOFF</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">    <span class="p">};</span></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="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">AdapterTrimmed</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c">            <span class="n" style="color: #333;">ATON</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c">            <span class="n" style="color: #333;">ATOFF</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c">            <span class="n" style="color: #333;">ATONLY</span></span>

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<td class="diff-line-num new new_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">

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

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<td class="diff-line-num new old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">    </span>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c">    <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">RunType</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c">            <span class="n" style="color: #333;">SINGLE</span><span class="p">,</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">            <span class="n" style="color: #333;">PAIRED</span><span class="p">,</span></span>

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<br>

</li>

<li id="1bee0e946e884ffe0c4bcf077071fc24e8887d09">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#1bee0e946e884ffe0c4bcf077071fc24e8887d09"><strong>src/Options.h</strong></a>

<hr>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,8 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">     </span>

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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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<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;">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;">umiTags</span><span class="p">,</span> <span class="n" style="color: #333;">logStdout</span><span class="p">;</span></span>

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

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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;">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="25" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC25" 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;">useRcTrimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimPostRm</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); 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="25" style="width: 35px; color: rgba(0,0,0,0.3); 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="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">interleavedInput</span><span class="p">,</span> <span class="n" style="color: #333;">htrimAdapterRm</span><span class="p">,</span> <span class="n" style="color: #333;">htrimMaxFirstOnly</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC25" 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;">useRcTrimEnd</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">addBarcodeAdapter</span></span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c">     <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">interleavedInput</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">iupacInput</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">htrimAdapterRm</span><span class="p">,</span> <span class="n" style="color: #333;">htrimMaxFirstOnly</span><span class="p">;</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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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<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;">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 class="n" style="color: #333;">p_min_overlap</span><span class="p">;</span></span>

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

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<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="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 class="n" style="color: #333;">htrimMinLength</span><span class="p">,</span> <span class="n" style="color: #333;">htrimMinLength2</span><span class="p">,</span> <span class="n" style="color: #333;">htrimMaxLength</span><span class="p">;</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,6 +44,7 @@ struct Options{</td>

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<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">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c">     <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RevCompMode</span>     <span class="n" style="color: #333;">rcMode</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c">     <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PairOverlap</span>     <span class="n" style="color: #333;">poMode</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c">     <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AdapterPreset</span>   <span class="n" style="color: #333;">aPreset</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c">     <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">AdapterTrimmed</span>  <span class="n" style="color: #333;">aTrimmed</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c">     </span>

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

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<pre style="margin: 0;"> <span id="LC49" 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;">concurrent_vector</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;">TBar</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">barcodes2</span><span class="p">,</span> <span class="n" style="color: #333;">adapters2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c">     </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,10 +81,12 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c">             <span class="n" style="color: #333;">logStdout</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="LC82" class="line" lang="c">             <span class="n" style="color: #333;">umiTags</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="LC83" class="line" lang="c">             <span class="n" style="color: #333;">interleavedInput</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c">             <span class="n" style="color: #333;">iupacInput</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="LC85" class="line" lang="c">             <span class="n" style="color: #333;">useStdin</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="LC86" class="line" lang="c">             <span class="n" style="color: #333;">useStdout</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="LC87" 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="LC88" class="line" lang="c">             <span class="n" style="color: #333;">useRcTrimEnd</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="LC89" class="line" lang="c">             <span class="n" style="color: #333;">addBarcodeAdapter</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="LC90" 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="LC91" class="line" lang="c">             <span class="n" style="color: #333;">htrimAdapterRm</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="LC92" class="line" lang="c">             <span class="n" style="color: #333;">htrimMaxFirstOnly</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 old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,6 +117,7 @@ struct Options{</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c">            <span class="n" style="color: #333;">arc_end</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c">            <span class="n" style="color: #333;">b_end</span>     <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">            <span class="n" style="color: #333;">aPreset</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">APOFF</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c">            <span class="n" style="color: #333;">aTrimmed</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ATON</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,7 +153,7 @@ const std::string getFlexbarURL(){</td>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"></span>

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

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" 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="nf" style="color: #900; font-weight: 600;">getFlexbarDescription</span><span class="p">(){</span></span>

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<td class="diff-line-num new_line old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. <span class="idiff left right">Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fasta and fastq format, e.g. from the Illumina platform</span>. Refer to the manual on github.com/seqan/flexbar/wiki or contact Johannes Roehr on github.com/jtroehr for support with this application."</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. <span class="idiff left right">Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided, e.g. trimming of homopolymers at read ends. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The software supports data in fasta and fastq format from multiple sequencing platforms</span>. Refer to the manual on github.com/seqan/flexbar/wiki or contact Johannes Roehr on github.com/jtroehr for support with this application."</span><span class="p">;</span></span>

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157

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -184,6 +188,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<pre style="margin: 0;"> <span id="LC188" 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;">"r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fasta/q file or stdin (-) with reads that may contain barcodes."</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 old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<pre style="margin: 0;"> <span id="LC189" 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;">"p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"reads2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Second input file of paired reads, gz and bz2 files supported."</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 old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

186

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<td class="diff-line-num new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<pre style="margin: 0;"> <span id="LC190" 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;">"i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"interleaved"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Interleaved format for first input set with paired reads."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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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;">"I"</span><span class="p">,</span> <span class="s" style="color: #d14;">"iupac"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Accept iupac symbols in reads and convert to N if not ATCG."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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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">

192

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

193

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<pre style="margin: 0;"> <span id="LC193" 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;">"Barcode detection"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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

194

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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;">"b"</span><span class="p">,</span>  <span class="s" style="color: #d14;">"barcodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fasta file with barcodes for demultiplexing, 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="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -214,7 +219,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="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;">"av"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-min-poverlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum overlap of paired reads for 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 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">

215

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

220

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<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;">"ac"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Include reverse complements of adapters."</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 old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

216

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<td class="diff-line-num new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

221

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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;">"ad"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use different trim-end for reverse complements of adapters."</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="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC222" 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;">"ab"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-add-barcode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Add reverse complement of detected barcode to adapters."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC223" 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;">"ar"</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;">"Consider only single read set for adapters."</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="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC224" 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;">"ak"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trimmed-out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Modify that trimmed reads are kept."</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 old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC225" 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;">"ay"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-cycles"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of adapter removal cycles."</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="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC226" 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;">"am"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-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>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="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;">"ai"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-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>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -257,7 +264,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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

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<pre style="margin: 0;"> <span id="LC264" 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;">"zip-output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Direct compression of output files."</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 old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC265" 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;">"1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stdout-reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Write reads to stdout, tagged and interleaved if needed."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="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;">"R"</span><span class="p">,</span> <span class="s" style="color: #d14;">"output-reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output file for reads instead of target prefix usage."</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;">OUTPUT_FILE</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC260" 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 right">D</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"output-reads2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output file for reads2 instead of target prefix usage."</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;">OUTPUT_FILE</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="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 right">P</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"output-reads2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output file for reads2 instead of target prefix usage."</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;">OUTPUT_FILE</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="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;">"j"</span><span class="p">,</span> <span class="s" style="color: #d14;">"length-dist"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Generate length distribution for read output files."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="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;">"s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"single-reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Write single reads for too short counterparts in pairs."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="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;">"S"</span><span class="p">,</span> <span class="s" style="color: #d14;">"single-reads-paired"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Write paired single reads with N for short counterparts."</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); 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="294" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -287,6 +294,8 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC294" 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-min-poverlap"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); 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="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC295" 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="289" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC296" 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-end"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC297" 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-add-barcode"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="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-trimmed-out"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); 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="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC299" 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-read-set"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); 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="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC300" 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-cycles"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num 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">

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

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<pre style="margin: 0;"> <span id="LC301" 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-match"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); 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="317" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -308,6 +317,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC317" 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;">"bundle"</span><span class="p">);</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC318" 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;">"bundles"</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC319" 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;">"interleaved"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); 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="320" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC320" 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;">"iupac"</span><span class="p">);</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC321" 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>

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<td class="diff-line-num old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC322" 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"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="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 unfold js-unfold old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -359,6 +369,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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<td class="diff-line-num old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); 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="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC370" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); 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="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC371" 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-revcomp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ON ONLY"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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;">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-trimmed-out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"OFF ONLY"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); 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="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC373" 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-pair-overlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ON SHORT ONLY"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); 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="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC374" 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-preset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TruSeq SmallRNA Methyl Ribo Nextera NexteraMP"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

364

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<td class="diff-line-num new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

375

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); 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="414" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -403,7 +414,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>

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403

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<td class="diff-line-num new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP reads.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-t</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP target </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-q</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP TAIL </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-qf</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP i1.8"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); 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="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP reads.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-b</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP barcodes.fa </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-bt</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP LTAIL"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP reads.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-a</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP adapters.fa </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-ao</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP 3 </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-ae</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP 0.1"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

406

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<td class="diff-line-num new_line old" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC406" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r1.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-p</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r2.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-a</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP a<span class="idiff left right">dapters</span>.fa </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-ap</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP ON"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); 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="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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

<pre style="margin: 0;">+<span id="LC417" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r1.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-p</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r2.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-a</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP a<span class="idiff left">1.fa </span></span><span class="se" style="color: #d14;"><span class="idiff">\\</span></span><span class="s" style="color: #d14;"><span class="idiff">fB-a2</span></span><span class="se" style="color: #d14;"><span class="idiff">\\</span></span><span class="s" style="color: #d14;"><span class="idiff right">fP a2</span>.fa </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-ap</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP ON"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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407

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c">    <span class="n" style="color: #333;">addText</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_toolDoc</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fBflexbar</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-r</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r1.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-p</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP r2.fq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-aa</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP TruSeq </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-ap</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP ON"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

408

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<td class="diff-line-num new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

419

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

409

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<td class="diff-line-num new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

420

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -613,6 +624,11 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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

613

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

624

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

</pre>

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

614

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<td class="diff-line-num new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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

615

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<td class="diff-line-num new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

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<pre style="margin: 0;"> <span id="LC626" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); 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="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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<pre style="margin: 0;">+<span id="LC627" 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;">"iupac"</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); 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="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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<pre style="margin: 0;">+<span id="LC628" 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;">"Iupac reads:           on"</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="616" style="width: 35px; color: rgba(0,0,0,0.3); 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="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="c">            <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">iupacInput</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="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); 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="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

631

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

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

632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="c">    </span>

</pre>

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

617

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

633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// barcode and adapter file options</span></span>

</pre>

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

618

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<td class="diff-line-num new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

634

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); 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="887" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -871,12 +887,10 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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<td class="diff-line-num old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

871

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<td class="diff-line-num new_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

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<td class="diff-line-num new_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<pre style="margin: 0;"> <span id="LC888" 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;">"output-reads"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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;">"output-reads2"</span><span class="p">)</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;">runType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SINGLE</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

873

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<td class="diff-line-num new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

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<pre style="margin: 0;"> <span id="LC889" 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;">outReadsFile</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"output-reads"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

874

</td>

<td class="diff-line-num new_line old" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC874" 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;">"output-reads:          "</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;">outReadsFile</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="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

</td>

<td class="diff-line-num new_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

</td>

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<pre style="margin: 0;"> <span id="LC890" class="line" lang="c">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

876

</td>

<td class="diff-line-num new_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

</td>

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

<pre style="margin: 0;"> <span id="LC891" class="line" lang="c">            </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

</td>

<td class="diff-line-num new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

</td>

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

<pre style="margin: 0;"> <span id="LC892" 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;">"output-reads2"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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;">"output-reads"</span><span class="p">)</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;">runType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

878

</td>

<td class="diff-line-num new_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

</td>

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

<pre style="margin: 0;"> <span id="LC893" 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;">outReadsFile2</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"output-reads2"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

879

</td>

<td class="diff-line-num new_line old" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC879" 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;">"output-reads2:         "</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;">outReadsFile2</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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

</td>

<td class="diff-line-num new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

</td>

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

<pre style="margin: 0;"> <span id="LC894" class="line" lang="c">                    </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

</td>

<td class="diff-line-num new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

</td>

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

<pre style="margin: 0;"> <span id="LC895" 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;">outReadsFile</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;">outReadsFile2</span><span class="p">){</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

</td>

<td class="diff-line-num new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

</td>

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

<pre style="margin: 0;"> <span id="LC896" 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;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Output reads and reads2 file should not be the same.</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>

</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="1043" style="width: 35px; color: rgba(0,0,0,0.3); 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="1057" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1043,6 +1057,22 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>

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<td class="diff-line-num old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1043

</td>

<td class="diff-line-num new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1057

</td>

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

<pre style="margin: 0;"> <span id="LC1057" class="line" lang="c">                           <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">relaxRegion</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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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1044

</td>

<td class="diff-line-num new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

</td>

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

<pre style="margin: 0;"> <span id="LC1058" class="line" lang="c">                   <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="diff-line-num new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1059

</td>

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

<pre style="margin: 0;"> <span id="LC1059" 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1060

</td>

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

<pre style="margin: 0;">+<span id="LC1060" 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;">"adapter-add-barcode"</span><span class="p">)</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;">isPaired</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;">a_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">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;">rcMode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">RCON</span> <span class="o" style="font-weight: 600;">&&</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1061

</td>

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

<pre style="margin: 0;">+<span id="LC1061" class="line" lang="c">                           <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BARCODE_READ</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;">barDetect</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BOFF</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_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>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1062

</td>

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

<pre style="margin: 0;">+<span id="LC1062" 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1063

</td>

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

<pre style="margin: 0;">+<span id="LC1063" 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;">"adapter-add-barcode:   on"</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1064

</td>

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

<pre style="margin: 0;">+<span id="LC1064" class="line" lang="c">                           <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">addBarcodeAdapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1065

</td>

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

<pre style="margin: 0;">+<span id="LC1065" class="line" lang="c">                   <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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1066

</td>

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

<pre style="margin: 0;">+<span id="LC1066" 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1067

</td>

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

<pre style="margin: 0;">+<span id="LC1067" 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;">"adapter-trimmed-out"</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1068

</td>

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

<pre style="margin: 0;">+<span id="LC1068" class="line" lang="c">                           <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a_trimmed_out</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1069

</td>

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

<pre style="margin: 0;">+<span id="LC1069" class="line" lang="c">                           <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">a_trimmed_out</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trimmed-out"</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1070

</td>

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

<pre style="margin: 0;">+<span id="LC1070" 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;">"adapter-trimmed-out:   "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">a_trimmed_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>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1071

</td>

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

<pre style="margin: 0;">+<span id="LC1071" 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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1072

</td>

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

<pre style="margin: 0;">+<span id="LC1072" class="line" lang="c">                                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trimmed_out</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"OFF"</span><span class="p">)</span>  <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">aTrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ATOFF</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1073

</td>

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

<pre style="margin: 0;">+<span id="LC1073" 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_trimmed_out</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ONLY"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">aTrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ATONLY</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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1074

</td>

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

<pre style="margin: 0;">+<span id="LC1074" class="line" lang="c">                   <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="1046" style="width: 35px; color: rgba(0,0,0,0.3); 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="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1075

</td>

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

<pre style="margin: 0;">+<span id="LC1075" class="line" lang="c">                   </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

</td>

<td class="diff-line-num new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1076

</td>

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

<pre style="margin: 0;"> <span id="LC1076" 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;">"adapter-read-set"</span><span class="p">)</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;">isPaired</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;">adapRm</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NORMAL2</span><span class="p">){</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1047

</td>

<td class="diff-line-num new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

</td>

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

<pre style="margin: 0;"> <span id="LC1077" class="line" lang="c">                           <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a_read_set</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

</td>

<td class="diff-line-num new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1078

</td>

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

<pre style="margin: 0;"> <span id="LC1078" class="line" lang="c">                           <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">a_read_set</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>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="39ce06c130af5661718537ce52c57783c42daa69">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#39ce06c130af5661718537ce52c57783c42daa69"><strong>src/PairedAlign.h</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">@@ -14,7 +14,7 @@ class PairedAlign : public tbb::filter {</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="nl">private:</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_writeUnassigned</span><span class="p">,</span> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">,</span> <span class="n" style="color: #333;">m_umiTags</span><span class="p">,</span> <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_htrim</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimAdapterRm</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimMaxFirstOnly</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="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_htrim</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimAdapterRm</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimMaxFirstOnly</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_addBarcodeAdapter</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     </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;">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_htrimLeft</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimRight</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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<td class="diff-line-num unfold js-unfold 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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,6 +61,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c">             <span class="n" style="color: #333;">m_umiTags</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">umiTags</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c">             <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useRcTrimEnd</span><span class="p">),</span></span>

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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>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c">             <span class="n" style="color: #333;">m_addBarcodeAdapter</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">addBarcodeAdapter</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_htrimLeft</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimLeft</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c">             <span class="n" style="color: #333;">m_htrimRight</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimRight</span><span class="p">),</span></span>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c">             <span class="n" style="color: #333;">m_htrimMinLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMinLength</span><span class="p">),</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,11 +107,11 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC107" 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 old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c">            <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">m_barType</span><span class="p">){</span></span>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

109

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BARCODE_READ</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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;">b</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ_REMOVAL2</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;">barID2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ_REMOVAL</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ2</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;">barID2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BARCODE_READ</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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;">b</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ_REMOVAL2</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;">barID2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ_REMOVAL</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span>  <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ2</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;">barID2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">WITHIN_READ</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BOFF</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c">            <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c">            </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,12 +126,49 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">            </span>

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<pre style="margin: 0;"> <span id="LC127" 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 new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c">            </span>

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<td class="diff-line-num new_line old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_adapRem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ATWO</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c">                    <span class="n" style="color: #333;">m_a1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_adapRem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ATWO</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c">                    </span>

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c">                    <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">addBarcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_addBarcodeAdapter</span> <span class="o" style="font-weight: 600;">&&</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="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barID2</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c">                            <span class="n" style="color: #333;">addBarcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_barcodes2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barID2</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;">seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c">                            </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_umiTags</span> <span class="o" style="font-weight: 600;">&&</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="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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" 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;">umiPos</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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" 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;">addBarcode</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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">addBarcode</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="sc" style="color: #d14;">'N'</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;">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 class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umiPos</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c">                                                    <span class="n" style="color: #333;">addBarcode</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;">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 class="n" style="color: #333;">umiPos</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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">                            <span class="n" style="color: #333;">seqan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">addBarcode</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c">                    <span class="n" style="color: #333;">m_a1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">addBarcode</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c">            </span>

</pre>

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

131

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c">            <span class="k" style="font-weight: 600;">if</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="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_adapRem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">AONE</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

132

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<td class="diff-line-num new_line old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC132" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_adapRem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NORMAL2</span><span class="p">)</span> <span class="n" style="color: #333;">m_a1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); 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="152" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC133" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span>                     <span class="n" style="color: #333;">m_a2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c">                    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c">                    <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">addBarcode</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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_addBarcodeAdapter</span> <span class="o" style="font-weight: 600;">&&</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c">                            <span class="n" style="color: #333;">addBarcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_barcodes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barID</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;">seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_umiTags</span> <span class="o" style="font-weight: 600;">&&</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="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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="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;">umiPos</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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<pre style="margin: 0;">+<span id="LC161" 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;">addBarcode</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">addBarcode</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="sc" style="color: #d14;">'N'</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;">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 class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umiPos</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c">                                                    <span class="n" style="color: #333;">addBarcode</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;">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 class="n" style="color: #333;">umiPos</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c">                                            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c">                                    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c">                            <span class="n" style="color: #333;">seqan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">addBarcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c">                    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c">                    </span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_adapRem</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NORMAL2</span><span class="p">)</span> <span class="n" style="color: #333;">m_a1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">addBarcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c">                    <span class="k" style="font-weight: 600;">else</span>                     <span class="n" style="color: #333;">m_a2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignSeqRead</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="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">alBundle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">cycle</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">idxAl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">alMode</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">addBarcode</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">            <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">    </span>

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<br>

</li>

<li id="5892684acbf66442a550859d89842772d4e04d36">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#5892684acbf66442a550859d89842772d4e04d36"><strong>src/PairedOutput.h</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +26,7 @@ private:</td>

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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="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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<pre style="margin: 0;"> <span id="LC27" 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;">BarcodeDetect</span>  <span class="n" style="color: #333;">m_barDetect</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="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;">QualTrimType</span>   <span class="n" style="color: #333;">m_qtrim</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="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;">AdapterTrimmed</span> <span class="n" style="color: #333;">m_aTrimmed</span><span class="p">;</span></span>

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

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<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>

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

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

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c">     <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">SeqOutput</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TSeqStr</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;">TSeqOutput</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c">     <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">SeqOutputFiles</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TSeqStr</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;">TOutFiles</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,6 +51,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC51" 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>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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_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>

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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="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="LC53" 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>

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<td class="diff-line-num new old_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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<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_aTrimmed</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">aTrimmed</span><span class="p">),</span></span>

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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="LC55" 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>

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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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" 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>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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_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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<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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,7 +241,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c">            </span>

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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">

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<pre style="margin: 0;"> <span id="LC242" 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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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c">            </span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c">            <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">l1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span>2ok</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="LC244" class="line" lang="c">            <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">r1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r</span>2ok</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="LC245" class="line" lang="c">            </span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c">            <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">m_runType</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC247" 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">@@ -253,11 +255,13 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC255" 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="LC256" class="line" lang="c">                                            <span class="p">}</span></span>

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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="LC256" 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="LC257" class="line" lang="c">                                                    </span>

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<pre style="margin: 0;">-<span id="LC258" 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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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c">                                            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC258" 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;">r1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">else</span> <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;">m_nShort_1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c">                                            </span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATOFF</span>  <span class="o" style="font-weight: 600;">&&</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">||</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;">rmAdapterRC</span><span class="p">))</span> <span class="n" style="color: #333;">r1ok</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="LC262" 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;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATONLY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapterRC</span><span class="p">)</span>  <span class="n" style="color: #333;">r1ok</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="LC263" class="line" lang="c">                                            </span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">r1ok</span><span class="p">)</span> <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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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c">                                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c">                            <span class="k" style="font-weight: 600;">break</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">@@ -284,14 +288,23 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC288" 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>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c">                                            <span class="p">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC287" 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;"><span class="idiff left right">l</span>1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC288" 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;"><span class="idiff left right">l</span>2ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC291" 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;"><span class="idiff left right">r</span>1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC292" 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;"><span class="idiff left right">r</span>2ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c">                                            </span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l1ok</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l2ok</span><span class="p">){</span></span>

</pre>

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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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">r1ok</span><span class="p">)</span> <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">m_nShort_1</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 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">

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">r2ok</span><span class="p">)</span> <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">m_nShort_2</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 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>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATOFF</span>  <span class="o" style="font-weight: 600;">&&</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">||</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;">rmAdapterRC</span> <span class="o" style="font-weight: 600;">||</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;">poRemoval</span><span class="p">))</span> <span class="n" style="color: #333;">r1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new 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="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;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATONLY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapterRC</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">poRemoval</span><span class="p">)</span>  <span class="n" style="color: #333;">r1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c">                                            </span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATOFF</span>  <span class="o" style="font-weight: 600;">&&</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">||</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;">rmAdapterRC</span> <span class="o" style="font-weight: 600;">||</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;">poRemoval</span><span class="p">))</span> <span class="n" style="color: #333;">r2ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new 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="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;">m_aTrimmed</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ATONLY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">rmAdapterRC</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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;">poRemoval</span><span class="p">)</span>  <span class="n" style="color: #333;">r2ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new 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 old_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">

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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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">r1ok</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r2ok</span><span class="p">){</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c">                                                    <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</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>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c">                                                    <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">f2</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;">r2</span><span class="p">);</span></span>

</pre>

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

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<td class="diff-line-num old old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC294" 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;"><span class="idiff left">l1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span>2ok</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC307" 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;"><span class="idiff left">r1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r</span>2ok</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); 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="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c">                                                    <span class="n" style="color: #333;">m_nSingleReads</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c">                                                    </span>

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<td class="diff-line-num old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c">                                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_writeSingleReads</span><span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -308,7 +321,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c">                                                            <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">f2</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;">r2</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c">                                                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c">                                            <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC311" 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="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;"><span class="idiff left">l1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span>2ok</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC324" 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="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;"><span class="idiff left">r1ok</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r</span>2ok</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c">                                                    <span class="n" style="color: #333;">m_nSingleReads</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -325,9 +338,6 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c">                                                            <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">f2</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;">r2</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="c">                                                    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c">                                            <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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">l1ok</span><span class="p">)</span> <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">m_nShort_1</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c">                                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">l2ok</span><span class="p">)</span> <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">outIdx</span><span class="p">].</span><span class="n" style="color: #333;">m_nShort_2</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c">                            <span class="p">}</span></span>

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

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<br>

</li>

<li id="62c9118c70f0995099615beb749b39099b0e417d">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#62c9118c70f0995099615beb749b39099b0e417d"><strong>src/QualTrimming.h</strong></a>

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,10 +43,10 @@ unsigned qualTrimming(const TString& qual, unsigned const _cutoff, Window const</td>

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

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">avg</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC47" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Work with a</span>bsolute cutoff in window to avoid divisions</span></span>

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

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c">     </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">A</span>bsolute cutoff in window to avoid divisions</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_cutoff</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">window</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"></span>

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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="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c">     <span class="c1" style="color: #998; font-style: italic;">// Calculate average quality of initial window</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c">     <span class="k" style="font-weight: 600;">for</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="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">window</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c">             <span class="n" style="color: #333;">avg</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getQuality</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,9 +57,15 @@ unsigned qualTrimming(const TString& qual, unsigned const _cutoff, Window const</td>

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

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c">             <span class="c1" style="color: #998; font-style: italic;">// Take care only not to go over the end of the sequence. Shorten window near the end</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c">             <span class="n" style="color: #333;">avg</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">getQuality</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c">             <span class="n" style="color: #333;">avg</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">window</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;">qual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">getQuality</span><span class="p">(</span><span class="n" style="color: #333;">qual</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;">window</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c">             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">window</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;">qual</span><span class="p">)){</span></span>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c">                     <span class="n" style="color: #333;">avg</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getQuality</span><span class="p">(</span><span class="n" style="color: #333;">qual</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;">window</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c">             <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c">             <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c">                     <span class="n" style="color: #333;">cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_cutoff</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;">qual</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="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c">             <span class="p">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">i </span>holds start of first window that turned bad</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c">     <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;">// holds start of first window that turned bad</span></span>

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

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<br>

</li>

<li id="2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd"><strong>src/SeqAlign.h</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ private:</td>

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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="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 old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); 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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" 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;">PairOverlap</span> <span class="n" style="color: #333;">m_poMode</span><span class="p">;</span></span>

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

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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_isBarcoding</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeTag</span><span class="p">,</span> <span class="n" style="color: #333;">m_umiTags</span><span class="p">,</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="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_isBarcoding</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeTag</span><span class="p">,</span> <span class="n" style="color: #333;">m_umiTags</span><span class="p">,</span> <span class="n" style="color: #333;">m_strictRegion</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_addBarcodeAdapter</span></span><span class="p">;</span></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="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 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_minOverlap</span><span class="p">,</span> <span class="n" style="color: #333;">m_tailLength</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" 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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<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="k" style="font-weight: 600;">const</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;">m_bundleSize</span><span class="p">;</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,6 +41,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c">                     <span class="n" style="color: #333;">m_log</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">logAlign</span><span class="p">),</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c">                     <span class="n" style="color: #333;">m_format</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">),</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c">                     <span class="n" style="color: #333;">m_writeTag</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="p">),</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c">                     <span class="n" style="color: #333;">m_addBarcodeAdapter</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">addBarcodeAdapter</span><span class="p">),</span></span>

</pre>

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<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">

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c">                     <span class="n" style="color: #333;">m_strictRegion</span><span class="p">(</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;">relaxRegion</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c">                     <span class="n" style="color: #333;">m_bundleSize</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">bundleSize</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">                     <span class="n" style="color: #333;">m_out</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">out</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">@@ -53,7 +54,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c">     <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c">     </span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c">     </span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignSeqRead</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;">sr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">performRemoval</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;">Alignments</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignments</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;">ComputeCycle</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cycle</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">idxAl</span><span class="p">,</span> <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;">AlignmentMode</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alMode</span><span class="p">,</span> <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;">TrimEnd</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignSeqRead</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;">sr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">performRemoval</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;">Alignments</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignments</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;">ComputeCycle</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cycle</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">idxAl</span><span class="p">,</span> <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;">AlignmentMode</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alMode</span><span class="p">,</span> <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;">TrimEnd</span> <span class="n" style="color: #333;">trimEnd</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TSeqStr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">addBarcode</span></span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c">             </span>

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<pre style="margin: 0;"> <span id="LC59" 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="LC60" 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="LC82" class="line" lang="c">                             <span class="k" style="font-weight: 600;">if</span>     <span class="p">(</span><span class="n" style="color: #333;">alMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ALIGNRCOFF</span> <span class="o" style="font-weight: 600;">&&</span>   <span class="n" style="color: #333;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">rcAdapter</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC83" 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;">alMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ALIGNRC</span>    <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">rcAdapter</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c">                             </span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c">                             <span class="n" style="color: #333;">TSeqStr</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">qseq</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c">                             <span class="n" style="color: #333;">TSeqStr</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">qseq</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span><span class="n" style="color: #333;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c">                             <span class="n" style="color: #333;">TSeqStr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c">                             <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c">                             <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">tmpq</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c">                             </span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c">                             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_isBarcoding</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_addBarcodeAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">addBarcode</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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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c">                                     <span class="n" style="color: #333;">tmpq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">addBarcode</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c">                                     <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">tmpq</span><span class="p">,</span> <span class="n" style="color: #333;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c">                                     <span class="n" style="color: #333;">qseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmpq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c">                             <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c">                             </span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c">                             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LTAIL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c">                                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailLength</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">m_tailLength</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;">m_tailLength</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;">qseq</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">                                     <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailLength</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">m_tailLength</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;">m_tailLength</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c">                                     </span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">                                     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tailLength</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">readLength</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c">                                             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">)</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">tailLength</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,7 +107,7 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c">                            <span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">(</span><span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">aset</span><span class="p">[</span><span class="n" style="color: #333;">idxAl</span><span class="p">]),</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">                            </span>

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

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c">                            <span class="n" style="color: #333;">assignSource</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">(</span><span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">aset</span><span class="p">[</span><span class="n" style="color: #333;">idxAl</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rseq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c">                            <span class="n" style="color: #333;">assignSource</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">(</span><span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">aset</span><span class="p">[</span><span class="n" style="color: #333;">idxAl</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c">                            <span class="n" style="color: #333;">assignSource</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">(</span><span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">aset</span><span class="p">[</span><span class="n" style="color: #333;">idxAl</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">qseq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c">                            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c">                            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">idxAl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c">                    <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -124,6 +131,11 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c">                    <span class="n" style="color: #333;">m_algo</span><span class="p">.</span><span class="n" style="color: #333;">alignGlobal</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">cycle</span><span class="p">,</span> <span class="n" style="color: #333;">idxAl</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">trimEnd</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">                    </span>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c">                    <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">queryLength</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;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</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="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_isBarcoding</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_addBarcodeAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">addBarcode</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="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">                            <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">queryLength</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;">addBarcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c">                    <span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">                    <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">tailLength</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">m_tailLength</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;">m_tailLength</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">queryLength</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">                    </span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">                    <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">overlapLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">endPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">startPos</span><span class="p">;</span></span>

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<br>

</li>

<li id="66f0e3b2db8f7898f9ac09c323e12f2e1acfe23d">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#66f0e3b2db8f7898f9ac09c323e12f2e1acfe23d"><strong>src/SeqAlignPair.h</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">@@ -114,6 +114,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c">                                    </span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c">                                    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_modified</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c">                                    </span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c">                                    <span class="n" style="color: #333;">seqRead2</span><span class="p">.</span><span class="n" style="color: #333;">poRemoval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c">                                    </span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_writeTag</span><span class="p">)</span> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead2</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">"_Flexbar_removal_PO"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c">                    <span class="p">}</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c">                                    <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_modified</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c">                                    </span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c">                                    <span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">poRemoval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">                                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_writeTag</span><span class="p">)</span> <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;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">"_Flexbar_removal_PO"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">                            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c">                    <span class="p">}</span></span>

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<br>

</li>

<li id="aa49d3edaf982a9eb8ecad9841b1507eba6ed69a">

<a href="https://salsa.debian.org/med-team/flexbar/compare/06a8d9bfad2bc8dfda7fb8a7b35b063eb13d6cac...299261d2beec41d20ce41e1701d01b302a72daa7#aa49d3edaf982a9eb8ecad9841b1507eba6ed69a"><strong>src/SeqInput.h</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">@@ -16,7 +16,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC16" 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;">QualTrimType</span> <span class="n" style="color: #333;">m_qtrim</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="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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">     </span>

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<td class="diff-line-num old old_line" 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_preProcess</span><span class="p">,</span> <span class="n" style="color: #333;">m_useStdin</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_preProcess</span><span class="p">,</span> <span class="n" style="color: #333;">m_useStdin</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_iupacInput</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" 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_maxUncalled</span><span class="p">,</span> <span class="n" style="color: #333;">m_preTrimBegin</span><span class="p">,</span> <span class="n" style="color: #333;">m_preTrimEnd</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="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_nrReads</span><span class="p">,</span> <span class="n" style="color: #333;">m_nrChars</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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<td class="diff-line-num unfold js-unfold 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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,6 +33,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC33" 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>

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<pre style="margin: 0;"> <span id="LC34" 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>

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<pre style="margin: 0;"> <span id="LC35" 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>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c">             <span class="n" style="color: #333;">m_iupacInput</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">iupacInput</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c">             <span class="n" style="color: #333;">m_format</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">),</span></span>

</pre>

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<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">

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<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">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c">             <span class="n" style="color: #333;">m_nrReads</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c">             <span class="n" style="color: #333;">m_nrChars</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,12 +77,30 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c">                             <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span>     <span class="n" style="color: #333;">nReads</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;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">-<span id="LC79" 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;">FASTA</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC80" class="line" lang="c">                                     <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c">                             <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_iupacInput</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="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;">FASTA</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c">                                             <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c">                                     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" 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 new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c">                                             <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c">                                             <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c">                                     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num 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">

81

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

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c">                             <span class="p">}</span></span>

</pre>

</td>

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

82

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

90

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<pre style="margin: 0;"> <span id="LC90" 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 old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

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<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC83" class="line" lang="c">                                     <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

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<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC84" class="line" lang="c">                                     <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c">                                     <span class="n" style="color: #333;">seqan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringSet</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seqan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IupacString</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqsIupac</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c">                                     </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c">                                     <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seqsIupac</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c">                                     </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="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;">FASTA</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">                                             <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqsIupac</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c">                                     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="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 new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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

<pre style="margin: 0;">+<span id="LC99" class="line" lang="c">                                             <span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c">                                            <span class="n" style="color: #333;">readRecords</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">,</span> <span class="n" style="color: #333;">seqsIupac</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">seqFileIn</span><span class="p">,</span> <span class="n" style="color: #333;">nReads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c">                                    <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqsIupac</span><span class="p">;</span></span>

</pre>

</td>

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

85

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC104" class="line" lang="c">                            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c">                            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<pre style="margin: 0;"> <span id="LC106" 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;">ids</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 unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,6 +152,7 @@ public:</td>

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

133

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

152

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">                                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c">                                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c">                            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

136

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c">                            <span class="n" style="color: #333;">m_nrReads</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;">ids</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c">                            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">);</span></span>

</pre>

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