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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/9856de0a96691831d1b7d2a34d0de5aa22a78425">9856de0a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-22T15:54:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/39e50e2c490110a5b36195a04430c198e4c7a79c">39e50e2c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-22T15:54:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.0'
Update to upstream version '3.2.0'
with Debian dir 44ed68dc0ba312efdbef414debb7d8900cb5ee9a</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/flexbar/commit/e6cb3be1f16a1b3fd448b72016fbbfede0571467">e6cb3be1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-22T15:54:34+02:00</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/6e3443441c2f480a838b07e7c722c2507db86230">6e344344</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-22T15:56:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>14 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>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#9d51a78783295e039ae9dbc298d048f0c6e01b63">
src/Flexbar.cpp
</a>
</li>
<li class="file-stats">
<a href="#e17337c7f2cf4f41795cb0478837b5fac99c82a8">
src/Flexbar.h
</a>
</li>
<li class="file-stats">
<a href="#e46cbf6df1dcc17df0ea6052697f523aefb88ff4">
src/FlexbarTypes.h
</a>
</li>
<li class="file-stats">
<a href="#e1246608ee12e7b825a45c6dd63be6b7c5c52c1a">
src/LoadFasta.h
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<li class="file-stats">
<a href="#1bee0e946e884ffe0c4bcf077071fc24e8887d09">
src/Options.h
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</li>
<li class="file-stats">
<a href="#39ce06c130af5661718537ce52c57783c42daa69">
src/PairedAlign.h
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<li class="file-stats">
<a href="#35b9932b85a450e1d8d94d54dc291117458373e3">
src/PairedInput.h
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<li class="file-stats">
<a href="#5892684acbf66442a550859d89842772d4e04d36">
src/PairedOutput.h
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<li class="file-stats">
<a href="#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd">
src/SeqAlign.h
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</li>
<li class="file-stats">
<a href="#e2dac719d776653f92cfaedf47045ae0c6d30b38">
src/SeqAlignAlgo.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/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ cmake_minimum_required( VERSION 2.8.2 )</td>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span> FLEXBAR <span class="p">)</span></span>
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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">
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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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<td class="line_content noteable_line 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">1</span>.0"</span> <span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="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">2</span>.0"</span> <span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">FLEXBAR_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/include <span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># link_directories( ${FLEXBAR_SOURCE_DIR}/lib )</span></span>
</pre>
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<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -28,20 +28,20 @@ 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="LC28" class="line" lang="markdown">Make sure that <span class="sb" style="color: #d14;">`cmake`</span> is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). 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>
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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">*</span> Get SeqAn library version 2.2.0 <span class="p">[</span><span class="nv" style="color: teal;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/seqan/releases/download/seqan-v2.2.0/seqan-library-2.2.0.tar.xz</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">1</span> source code <span class="p">[</span><span class="nv" style="color: teal;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> Download Flexbar 3.<span class="idiff left right">2</span> source code <span class="p">[</span><span class="nv" style="color: teal;">release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/releases</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">Decompress both files:</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tar xzf flexbar-3.<span class="idiff left right">1</span>.0.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tar xzf flexbar-3.<span class="idiff left right">2</span>.0.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tar xJf seqan-library-2.2.0.tar.xz</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">Move SeqAn include folder to Flexbar:</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mv seqan-library-2.2.0/include flexbar-3.<span class="idiff left right">1</span>.0</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> mv seqan-library-2.2.0/include flexbar-3.<span class="idiff left right">2</span>.0</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown">Use these commands for building:</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd flexbar-3.<span class="idiff left right">1</span>.0</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd flexbar-3.<span class="idiff left right">2</span>.0</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cmake .</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make</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">@@ -77,9 +77,9 @@ In this example, reads that are barcoded on left side are demultiplexed by speci</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;"> flexbar -r reads.fq -t target -b brc.fa -be LTAIL -a adp.fa</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown">The second example shows how to trim compressed reads based on their quality scores in illumina version 1.8 format. Afterwards, provided adapters are removed in right trim-end mode, only if the overlap of adapter and read has at least length <span class="idiff left right">five with at most 4</span>0% errors.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">The second example shows how to trim compressed reads based on their quality scores in illumina version 1.8 format. Afterwards, provided adapters are removed in right trim-end mode, only if the overlap of adapter and read has at least length <span class="idiff left right">5 with at most 2</span>0% errors.</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;"> flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;"> flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">For further examples visit the <span class="p">[</span><span class="nv" style="color: teal;">manual</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/flexbar/wiki</span><span class="p">)</span> page.</span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">flexbar (1:3.2.0-1) unstable; urgency=medium</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="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 22 May 2018 15:54:36 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">flexbar (1:3.1.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#9d51a78783295e039ae9dbc298d048f0c6e01b63"><strong>src/Flexbar.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,9 @@</td>
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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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<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>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Version 3.1.0</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 3.2.0</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>
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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>
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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uses SeqAn library release 2.2.0</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> and TBB library 4.0 or later</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">@@ -27,8 +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="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"3.<span class="idiff left right">1</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">April</span> 2018"</span><span class="p">;</span></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">2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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</span> 2018"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="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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<li id="e17337c7f2cf4f41795cb0478837b5fac99c82a8">
<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#e17337c7f2cf4f41795cb0478837b5fac99c82a8"><strong>src/Flexbar.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">@@ -98,17 +98,18 @@ void loadAdapters(Options &o, const bool secondSet, const bool useAdapterFile){</td>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cmdline"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">adapterSeq</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">adapters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bar</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC106" 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;">revCompAdapter</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC101" 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;">rcMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RCOFF</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="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cmdline"</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">adapterSeq</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">adapters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bar</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="p">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" 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;">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 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;">RCONLY</span><span class="p">){</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">adapterSeqRC</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;">adapterSeq</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" 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;">adapterSeqRC</span><span class="p">);</span></span>
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109
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">barRC</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cmdline<span class="idiff left right"> revcomp</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cmdline<span class="idiff left right">_rc</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapterSeqRC</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">adapters</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">barRC</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#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">@@ -11,17 +11,21 @@ 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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13
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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>
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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="LC17" class="line" lang="c"> <span class="n" style="color: #333;">umi</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="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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<pre style="margin: 0;"> <span id="LC24" 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="LC25" 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="LC26" 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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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">umi</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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="LC28" 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="LC29" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC31" 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">@@ -60,7 +64,7 @@ struct AlignResults{</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">overlapLength</span><span class="p">,</span> <span class="n" style="color: #333;">queryLength</span><span class="p">,</span> <span class="n" style="color: #333;">tailLength</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">allowedErrors</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;">TSeqStr</span> <span class="n" style="color: #333;"><span class="idiff left right">rand</span>Tag</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;"><span class="idiff left right">umi</span>Tag</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alString</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">AlignResults</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">@@ -116,21 +120,35 @@ namespace flexbar{</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC121" 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>
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<pre style="margin: 0;"> <span id="LC122" 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="LC123" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">rcAdapter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC125" 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;">rmOverlap</span><span class="p">,</span> <span class="n" style="color: #333;">rmFull</span><span class="p">;</span></span>
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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;">TBar</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">rmOverlap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">rmFull</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">rmFull</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">rcAdapter</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="LC131" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> </span>
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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="LC129" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ComputeCycle</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">PRELOAD</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">COMPUTE</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">RESULTS</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c"> <span class="p">};</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">RevCompMode</span> <span class="p">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">RCOFF</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">RCON</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">RCONLY</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="p">};</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">AlignmentMode</span> <span class="p">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">ALIGNALL</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">ALIGNRCOFF</span><span class="p">,</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">ALIGNRC</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="p">};</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ComputeCycle</span> <span class="p">{</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">PRELOAD</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">COMPUTE</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">RESULTS</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="p">};</span></span>
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134
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> </span>
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135
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">LogAlign</span> <span class="p">{</span></span>
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136
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">NONE</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#e1246608ee12e7b825a45c6dd63be6b7c5c52c1a"><strong>src/LoadFasta.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">@@ -12,16 +12,16 @@ private:</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" 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;">bars</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_revComp</span><span class="p">,</span> <span class="n" style="color: #333;">m_isAdapter</span><span class="p">;</span></span>
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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;">bool</span> <span class="n" style="color: #333;">m_isAdapter</span><span class="p">;</span></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;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RevCompMode</span> <span class="n" style="color: #333;">m_rcMode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"> <span class="n" style="color: #333;">LoadFasta</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</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;">isAdapter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"> <span class="n" style="color: #333;">m_rcMode</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">rcMode</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">m_isAdapter</span><span class="p">(</span><span class="n" style="color: #333;">isAdapter</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">m_revComp</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;">revCompAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isAdapter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC27" 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">@@ -64,21 +64,24 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">idMap</span><span class="p">[</span><span class="n" style="color: #333;">ids</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ids</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="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">bars</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bar</span><span class="p">);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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_isAdapter</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_rcMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RCOFF</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_rcMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RCON</span><span class="p">){</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">bar</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">bar</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">bars</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bar</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="p">}</span></span>
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71
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_revComp</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</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="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">m_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 class="n" style="color: #333;">m_rcMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RCONLY</span><span class="p">)){</span></span>
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74
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">TSeqStr</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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75
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right"> revcomp</span>"</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;">append</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_rc</span>"</span><span class="p">);</span></span>
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77
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<pre style="margin: 0;"> <span id="LC79" 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;">seq</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> </span>
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79
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">TBar</span> <span class="n" style="color: #333;">barRC</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</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;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">barRC</span><span class="p">.</span><span class="n" style="color: #333;">rcAdapter</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="LC85" class="line" lang="c"> <span class="n" style="color: #333;">bars</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">barRC</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#1bee0e946e884ffe0c4bcf077071fc24e8887d09"><strong>src/Options.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">@@ -17,20 +17,21 @@ struct Options{</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">readsFile</span><span class="p">,</span> <span class="n" style="color: #333;">readsFile2</span><span class="p">,</span> <span class="n" style="color: #333;">barReadsFile</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">barcodeFile</span><span class="p">,</span> <span class="n" style="color: #333;">adapterFile</span><span class="p">,</span> <span class="n" style="color: #333;">barcode2File</span><span class="p">,</span> <span class="n" style="color: #333;">adapter2File</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">adapterSeq</span><span class="p">,</span> <span class="n" style="color: #333;">targetName</span><span class="p">,</span> <span class="n" style="color: #333;">logAlignStr</span><span class="p">,</span> <span class="n" style="color: #333;">outCompression</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;"><span class="idiff left">trimLeftNucs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimRightNucs</span></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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;"><span class="idiff left">htrimLeft</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">htrimRight</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">useAdapterFile</span><span class="p">,</span> <span class="n" style="color: #333;">useNumberTag</span><span class="p">,</span> <span class="n" style="color: #333;">useRemovalTag</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">randTag</span></span><span class="p">,</span> <span class="n" style="color: #333;">logStdout</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">useAdapterFile</span><span class="p">,</span> <span class="n" style="color: #333;">useNumberTag</span><span class="p">,</span> <span class="n" style="color: #333;">useRemovalTag</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">umiTags</span></span><span class="p">,</span> <span class="n" style="color: #333;">logStdout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">switch2Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">writeUnassigned</span><span class="p">,</span> <span class="n" style="color: #333;">writeSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">writeSingleReadsP</span><span class="p">,</span> <span class="n" style="color: #333;">writeLengthDist</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useStdin</span><span class="p">,</span> <span class="n" style="color: #333;">useStdout</span><span class="p">,</span> <span class="n" style="color: #333;">relaxRegion</span><span class="p">,</span> <span class="n" style="color: #333;">revCompAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimPostRm</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useStdin</span><span class="p">,</span> <span class="n" style="color: #333;">useStdout</span><span class="p">,</span> <span class="n" style="color: #333;">relaxRegion</span><span class="p">,</span> <span class="n" style="color: #333;">useRcTrimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimPostRm</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"> <span 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>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">qtrimWinSize</span><span class="p">,</span> <span class="n" style="color: #333;">a_overhang</span><span class="p">,</span> <span class="n" style="color: #333;">h<span class="idiff left right">psMinLength</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">h<span class="idiff left">trimMinLength</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">htrimMaxLength</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">a_cycles</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxUncalled</span><span class="p">,</span> <span class="n" style="color: #333;">min_readLen</span><span class="p">,</span> <span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">nThreads</span><span class="p">,</span> <span class="n" style="color: #333;">bundleSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">b_gapCost</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">b_errorRate</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">b_errorRate</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">h_errorRate</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC33" 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;">TrimEnd</span> <span class="n" style="color: #333;"><span class="idiff left">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">b</span>_end</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;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TrimEnd</span> <span class="n" style="color: #333;"><span class="idiff left">a_end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">b_end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">arc</span>_end</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;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileFormat</span> <span class="n" style="color: #333;">format</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;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QualityType</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" 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;">QualTrimType</span> <span class="n" style="color: #333;">qTrim</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">@@ -39,6 +40,7 @@ struct Options{</td>
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<pre style="margin: 0;"> <span id="LC40" 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;">RunType</span> <span class="n" style="color: #333;">runType</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" 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;">BarcodeDetect</span> <span class="n" style="color: #333;">barDetect</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" 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;">AdapterRemoval</span> <span class="n" style="color: #333;">adapRm</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC45" 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="LC46" 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">@@ -54,8 +56,8 @@ struct Options{</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">barcode2File</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">adapter2File</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">outCompression</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">trimLeftNucs</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">trimRightNucs</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">htrimLeft</span></span><span class="idiff right"> </span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">htrimRight</span></span><span class="idiff right"> </span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">isPaired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">useAdapterFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,23 +69,25 @@ struct Options{</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">writeLengthDist</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="LC70" class="line" lang="c"> <span class="n" style="color: #333;">switch2Fasta</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="LC71" 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="LC70" class="line" lang="c"> <span class="n" style="color: #333;">randTag</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="LC72" 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="LC73" 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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<pre style="margin: 0;"> <span id="LC74" 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="LC75" 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="LC76" class="line" lang="c"> <span class="n" style="color: #333;">relaxRegion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">revCompAdapter</span></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="LC77" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">useRcTrimEnd</span></span><span class="idiff right"> </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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75
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78
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<pre style="margin: 0;"> <span id="LC78" 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="LC76" class="line" lang="c"> </span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_read</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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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">qtrimThresh</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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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">qtrimWinSize</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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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"> <span class="n" style="color: #333;">a_tail_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">b_tail_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">b_min_overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">a_errorRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" 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="LC80" 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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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">qtrimThresh</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="LC86" class="line" lang="c"> <span class="n" style="color: #333;">qtrimWinSize</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="LC87" class="line" lang="c"> <span class="n" style="color: #333;">a_tail_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">b_tail_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">b_min_overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">htrimMaxLength</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="LC91" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FASTA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SANGER</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,6 +96,7 @@ struct Options{</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="n" style="color: #333;">cmprsType</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;">UNCOMPRESSED</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">barDetect</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;">BOFF</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;">adapRm</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;">AOFF</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">rcMode</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;">RCOFF</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC102" 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">@@ -117,7 +122,7 @@ const std::string getFlexbarBanner(const seqan::CharString version){</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC124" 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;">getFlexbarCitation</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<span class="idiff left">Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Flexbar - flexible barcode and adapter processing for next-generation</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">sequencing platforms. Biology 2012, 1(3):895-905</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<span class="idiff left">Johannes T. Roehr, Christoph Dieterich, Knut Reinert:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Flexbar 3.0 - SIMD and multicore parallelization. Bioinformatics 2017.</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Flexbar - flexible barcode and adapter processing for next-generation</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">sequencing platforms. Biology 2012</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"><span class="p">}</span></span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"></span>
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123
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128
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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 unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,10 +142,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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137
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"> </span>
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138
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setCitation(parser, "\n\n" + getFlexbarCitation());</span></span>
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139
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> </span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setAppName(parser, "");</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setShortCopyright(parser, "");</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setAppName(parser, "<span class="idiff left right">Flexbar</span>");</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setShortCopyright(parser, "<span class="idiff left right">BSD 3-Clause License</span>");</span></span>
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142
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setLongCopyright(parser, "");</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// ARG::OUTPUTPREFIX</span></span>
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144
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> </span>
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145
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">setShortDescription</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"flexible barcode and adapter removal"</span><span class="p">);</span></span>
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146
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -148,23 +152,24 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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148
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> </span>
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149
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<pre style="margin: 0;"> <span id="LC153" 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;">"hm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"man-help"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Print advanced options as man document."</span><span class="p">));</span></span>
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150
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154
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<pre style="margin: 0;"> <span id="LC154" 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;">"v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"versions"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Print Flexbar and SeqAn version numbers."</span><span class="p">));</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" 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;">"c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cite"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show program reference for citation."</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC155" 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;">"c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cite"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show program reference<span class="idiff left right">s</span> for citation."</span><span class="p">));</span></span>
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152
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> </span>
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153
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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 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;">"Basic options"</span><span class="p">);</span></span>
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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 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;">"n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of threads to employ."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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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 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;">"N"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bundle"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Number of read pairs per thread."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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156
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<td class="diff-line-num new_line old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC156" 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;">"t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Prefix for output file names or paths."</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;"><span class="idiff left right">STRING</span></span><span class="p">));</span></span>
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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">
160
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<pre style="margin: 0;">+<span id="LC160" 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;">"t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Prefix for output file names or paths."</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;"><span class="idiff left right">OUTPUT_PREFIX</span></span><span class="p">));</span></span>
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157
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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<pre style="margin: 0;"> <span id="LC161" 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>
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158
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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="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>
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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">
163
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<pre style="margin: 0;">+<span id="LC163" 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>
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159
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> </span>
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160
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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="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>
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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="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>
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162
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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="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;">"b2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcodes2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Additional barcodes file for second read set in paired mode."</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>
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163
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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="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;">"br"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-reads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fasta/q file containing separate barcode 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;">INPUT_FILE</span><span class="p">));</span></span>
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164
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<td class="diff-line-num new_line old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC164" 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;">"be"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-trim-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Type of detection, see section trim-end modes."</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>
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165
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<td class="diff-line-num new_line old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC165" 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;">"bn"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-tail-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Region size in tail trim-end modes. Default: barcode length."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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166
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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bo"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-min-overlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum overlap of barcode and read. Default: barcode length."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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167
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error rate threshold for mismatches and gaps."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DOUBLE</span><span class="p">));</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"be"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-trim-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Type of detection, see section trim-end modes."</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>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bn"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-tail-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Region size in tail trim-end modes. Default: barcode length."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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168
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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-keep"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Keep barcodes within reads instead of removal."</span><span class="p">));</span></span>
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169
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bu"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-unassigned"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Include unassigned reads in output generation."</span><span class="p">));</span></span>
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170
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"bm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-match"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment match score."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,14 +180,17 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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175
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapters"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fasta file with adapters for removal that may contain N."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">));</span></span>
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176
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181
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<pre style="margin: 0;"> <span id="LC181" 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;">"a2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapters2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"File with extra adapters for second read set in paired mode."</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>
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177
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182
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<pre style="margin: 0;"> <span id="LC182" 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;">"as"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-seq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Single adapter sequence as alternative to adapters option."</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>
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178
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<pre style="margin: 0;">-<span id="LC178" 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>
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179
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<pre style="margin: 0;">-<span id="LC179" 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;">"Consider also reverse complement of each adapter in search."</span><span class="p">));</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("ap", "adapter-pair-overlap", "Overlap detection for paired reads.", ARG::STRING));</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" 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;">"ao"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-min-overlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum overlap of adapter and read for removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" 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;">"at"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error rate threshold for mismatches and gaps."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DOUBLE</span><span class="p">));</span></span>
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180
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186
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<pre style="margin: 0;"> <span id="LC186" 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;">"ae"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trim-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Type of removal, see section trim-end modes."</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>
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181
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187
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<pre style="margin: 0;"> <span id="LC187" 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;">"an"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-tail-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Region size for tail trim-end modes. Default: adapter length."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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182
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("ah", "adapter-overhang", "Overhang at read ends in right and left modes.", ARG::INTEGER));</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" 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-relaxed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Skip restriction to pass read ends in right and left modes."</span><span class="p">));</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" 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;">"ao"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-min-overlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum overlap of adapter and read for removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" 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;">"at"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error rate threshold for mismatches and gaps."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DOUBLE</span><span class="p">));</span></span>
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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;">"ax"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-relaxed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Skip restriction to pass read ends in right and left modes."</span><span class="p">));</span></span>
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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;">"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>
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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;">"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 complement 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>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"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>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"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>
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186
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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;">"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>
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187
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"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>
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188
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"ag"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-gap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Alignment gap score."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,9 +199,6 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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191
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"u"</span><span class="p">,</span> <span class="s" style="color: #d14;">"max-uncalled"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Allowed uncalled bases N for each read."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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192
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pre-trim-left"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim given number of bases on 5' read end before detection."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pre-trim-right"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim specified number of bases on 3' end prior to detection."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on the left read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"Y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on the right read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"Z"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum length of homopolymers at read ends."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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197
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"k"</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim to specified read length from 3' end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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198
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"min-read-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum read length to remain after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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199
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -201,10 +206,18 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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201
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206
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<pre style="margin: 0;"> <span id="LC206" 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;">"q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Quality-based trimming mode."</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>
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202
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207
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<pre style="margin: 0;"> <span id="LC207" 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;">"qf"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-format"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Quality format."</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>
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203
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<td class="diff-line-num new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
208
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<pre style="margin: 0;"> <span id="LC208" 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;">"qt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-threshold"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum quality as threshold for trimming."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// addOption(parser, ArgParseOption("qm", "qtrim-win-mean", "Different threshold for min mean quality of window.", ARG::INTEGER));</span></span>
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205
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209
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<pre style="margin: 0;"> <span id="LC209" 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;">"qw"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-win-size"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Region size for sliding window approach."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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206
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210
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<pre style="margin: 0;"> <span id="LC210" 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;">"qa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-post-removal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Perform quality-based trimming after removal steps."</span><span class="p">));</span></span>
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207
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> </span>
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212
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<pre style="margin: 0;">+<span id="LC212" 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;">"Trimming of homopolymers"</span><span class="p">);</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-left"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on left read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>
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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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"Y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-right"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim certain homopolymers on right read end after removal."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">STRING</span><span class="p">));</span></span>
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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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-min-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Minimum length of homopolymers at read ends."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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<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="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;">"L"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-max-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum length of homopolymers at read ends."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INTEGER</span><span class="p">));</span></span>
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<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">
217
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<pre style="margin: 0;">+<span id="LC217" 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;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-max-first"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Max length of homopolymers only for first type."</span><span class="p">));</span></span>
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<td class="diff-line-num new old_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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<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">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error rate threshold for mismatches."</span><span class="p">,</span> <span class="n" style="color: #333;">ARG</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DOUBLE</span><span class="p">));</span></span>
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<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">
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;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-adapter"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trim only in case of adapter removal on same side."</span><span class="p">));</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c"> </span>
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208
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221
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<pre style="margin: 0;"> <span id="LC221" 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;">"Output selection"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
209
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222
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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;">"f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta-output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Prefer non-quality format fasta for output."</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
210
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223
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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;">"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>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -218,7 +231,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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218
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stdout-log"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Write statistics to console instead of target log file."</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
219
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<td class="diff-line-num new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"removal-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Tag reads that are subject to adapter or barcode removal."</span><span class="p">));</span></span>
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220
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<td class="diff-line-num new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"number-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Replace read tags by ascending number to save space."</span><span class="p">));</span></span>
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221
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<td class="diff-line-num new_line old" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">i</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"umi-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Capture UMIs in reads at barcode or adapter N positions."</span><span class="p">));</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">
234
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<pre style="margin: 0;">+<span id="LC234" 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;">"umi-tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Capture UMIs in reads at barcode or adapter N positions."</span><span class="p">));</span></span>
</pre>
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222
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"> </span>
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c"> </span>
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224
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">hideOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"version"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -232,23 +245,27 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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232
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-gap"</span><span class="p">);</span></span>
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233
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> </span>
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234
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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp"</span><span class="p">);</span></span>
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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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp-end"</span><span class="p">);</span></span>
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235
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<td class="diff-line-num new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-tail-length"</span><span class="p">);</span></span>
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236
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setAdvanced(parser, "adapter-overhang");</span></span>
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237
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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
251
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<pre style="margin: 0;"> <span id="LC251" 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-relaxed"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
238
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-read-set"</span><span class="p">);</span></span>
</pre>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-cycles"</span><span class="p">);</span></span>
</pre>
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239
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-match"</span><span class="p">);</span></span>
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240
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-mismatch"</span><span class="p">);</span></span>
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241
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-gap"</span><span class="p">);</span></span>
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242
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> </span>
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243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
244
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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">);</span></span>
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245
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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">);</span></span>
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246
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<td class="diff-line-num new_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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
247
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<td class="diff-line-num new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-win-size"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
248
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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">setAdvanced</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-post-removal"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" 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;">"htrim-left"</span><span class="p">);</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" 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;">"htrim-max-length"</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" 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;">"htrim-max-first"</span><span class="p">);</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" 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;">"htrim-adapter"</span><span class="p">);</span></span>
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249
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> </span>
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250
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266
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<pre style="margin: 0;"> <span id="LC266" 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;">"man-help"</span><span class="p">);</span></span>
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251
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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<pre style="margin: 0;"> <span id="LC267" 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>
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268
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<pre style="margin: 0;">+<span id="LC268" 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>
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252
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269
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<pre style="margin: 0;"> <span id="LC269" 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;">"stdout-reads"</span><span class="p">);</span></span>
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253
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270
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<pre style="margin: 0;"> <span id="LC270" 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>
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254
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271
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<pre style="margin: 0;"> <span id="LC271" 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>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -294,7 +311,9 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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294
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311
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<pre style="margin: 0;"> <span id="LC311" 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;">"qtrim-format"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sanger solexa i1.3 i1.5 i1.8"</span><span class="p">);</span></span>
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295
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312
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<pre style="margin: 0;"> <span id="LC312" 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;">"align-log"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ALL MOD TAB"</span><span class="p">);</span></span>
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296
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<td class="diff-line-num new_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">
313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"zip-output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GZ BZ2"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setValidValues(parser, "adapter-pair-overlap", "ON ONLY");</span></span>
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297
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<td class="diff-line-num new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-read-set"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1 2"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" 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>
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298
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> </span>
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299
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">,</span> <span class="s" style="color: #d14;">"flexbarOut"</span><span class="p">);</span></span>
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300
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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">
319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -302,7 +321,6 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
302
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<td class="diff-line-num 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">
321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
303
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<td class="diff-line-num new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"max-uncalled"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
304
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<td class="diff-line-num new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"min-read-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"18"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
305
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<td class="diff-line-num new_line old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
306
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<td class="diff-line-num new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
307
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<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">
325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-trim-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">);</span></span>
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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">
308
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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.0"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -313,6 +331,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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<td class="diff-line-num old_line" data-linenumber="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">
313
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<td class="diff-line-num new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trim-end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
314
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<td class="diff-line-num new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-min-overlap"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
315
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<td class="diff-line-num new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.1"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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">
334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-cycles"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
316
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<td class="diff-line-num new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// setDefaultValue(parser, "adapter-overhang", "0");</span></span>
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<td class="diff-line-num old_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">
317
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<td class="diff-line-num new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-match"</span><span class="p">,</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
318
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<td class="diff-line-num new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-mismatch"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-1"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -321,6 +340,8 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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<td class="diff-line-num old_line" data-linenumber="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">
321
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<td class="diff-line-num new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-threshold"</span><span class="p">,</span> <span class="s" style="color: #d14;">"20"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
322
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<td class="diff-line-num new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"qtrim-win-size"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
323
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"> </span>
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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">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-min-length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">setDefaultValue</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-error-rate"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0.1"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">addTextSection</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"TRIM-END MODES"</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" 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;">fBANY:</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP longer side of read remains after removal of overlap"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -331,7 +352,7 @@ void defineOptions(seqan::ArgumentParser &parser, const std::string version, con</td>
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331
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"> </span>
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332
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">addTextSection</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"EXAMPLES"</span><span class="p">);</span></span>
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333
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354
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<pre style="margin: 0;"> <span id="LC354" 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-b</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP brc.fa </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-be</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP LTAIL </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 adp.fa"</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="LC334" 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.gz </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="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 adp.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 5 </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-at</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP 0.<span class="idiff left right">4</span>"</span><span class="p">);</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" 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.gz </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="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 adp.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 5 </span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fB-at</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">fP 0.<span class="idiff left right">2</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"></span>
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); 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="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -458,9 +479,19 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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458
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479
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<pre style="margin: 0;"> <span id="LC479" 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;">nThreads</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">);</span></span>
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459
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480
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<pre style="margin: 0;"> <span id="LC480" 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;">"Number of threads: "</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;">nThreads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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460
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> </span>
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482
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<pre style="margin: 0;">+<span id="LC482" 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;">nThreads</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" 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;">"Number of threads should be 1 at least.</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>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"> <span class="p">}</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="c"> </span>
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461
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487
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<pre style="margin: 0;"> <span id="LC487" 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;">bundleSize</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>
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462
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488
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<pre style="margin: 0;"> <span id="LC488" 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;">"Bundled fragments: "</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;">bundleSize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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463
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> </span>
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490
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<pre style="margin: 0;">+<span id="LC490" 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;">bundleSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<td class="diff-line-num 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="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;">"Bundle size should be 1 at least.</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>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="c"> <span class="p">}</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="c"> </span>
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495
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<pre style="margin: 0;"> <span id="LC495" 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;">targetName</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"target"</span><span class="p">);</span></span>
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465
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496
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<pre style="margin: 0;"> <span id="LC496" 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;">"Target name: "</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;">targetName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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466
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -481,7 +512,20 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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481
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="c"> </span>
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482
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="c"> <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>
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483
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="c"> </span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> </span>
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516
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<pre style="margin: 0;">+<span id="LC516" 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;">"interleaved"</span><span class="p">)){</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" 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;">"Interleaved reads: on (paired run)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"> <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>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">interleavedInput</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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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> <span class="p">}</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"> </span>
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484
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523
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<pre style="margin: 0;"> <span id="LC523" 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;">"reads2"</span><span class="p">)){</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"> </span>
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525
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<pre style="margin: 0;">+<span id="LC525" 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;">interleavedInput</span><span class="p">){</span></span>
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<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="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;">"Please specify either interleaved reads or second reads file.</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>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="p">}</span></span>
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485
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529
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<pre style="margin: 0;"> <span id="LC529" 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;">readsFile2</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"reads2"</span><span class="p">);</span></span>
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486
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530
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<pre style="margin: 0;"> <span id="LC530" 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;">"Reads file 2: "</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;">readsFile2</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (paired run)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
487
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<td class="diff-line-num new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"> <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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -491,7 +535,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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491
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="n" style="color: #333;">checkInputType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">readsFile2</span><span class="p">,</span> <span class="n" style="color: #333;">fformat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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492
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> </span>
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493
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537
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<pre style="margin: 0;"> <span id="LC537" 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;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fformat</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
494
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<pre style="margin: 0;">-<span id="LC494" 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 class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"First and second reads file do not have same format.</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>
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<td class="diff-line-num new old_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">
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<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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<pre style="margin: 0;">+<span id="LC538" 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;">"First and second reads file do not have same format.</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>
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495
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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496
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
497
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<td class="diff-line-num new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
541
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<pre style="margin: 0;"> <span id="LC541" 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="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -509,7 +553,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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509
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<td class="diff-line-num new_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="c"> <span class="n" style="color: #333;">checkInputType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barReadsFile</span><span class="p">,</span> <span class="n" style="color: #333;">fformat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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510
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
511
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<td class="diff-line-num new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
555
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<pre style="margin: 0;"> <span id="LC555" 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;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fformat</span><span class="p">){</span></span>
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512
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<td class="diff-line-num new_line old" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC512" 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 class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Barcode reads file does not have same format as reads.</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>
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<td class="diff-line-num new old_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">
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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">
556
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<pre style="margin: 0;">+<span id="LC556" 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;">"Barcode reads file does not have same format as reads.</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>
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513
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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514
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"> <span class="p">}</span></span>
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515
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -570,19 +614,6 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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570
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC614" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"pre-trim-right: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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571
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="c"> <span class="p">}</span></span>
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572
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="c"> </span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">)){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
574
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<td class="diff-line-num new_line old" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-left-hps"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
575
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<td class="diff-line-num new_line old" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-left-hps: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"> <span class="p">}</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="c"> </span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">)){</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-right-hps"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-right-hps: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"> <span class="p">}</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="c"> </span>
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583
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<td class="diff-line-num new_line old" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-hps-length"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
584
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<td class="diff-line-num new_line old" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-hps-length: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"> </span>
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586
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">)){</span></span>
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<td class="diff-line-num old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
587
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"post-trim-length"</span><span class="p">);</span></span>
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588
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<td class="diff-line-num new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"post-trim-length: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -596,6 +627,11 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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596
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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597
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="p">}</span></span>
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598
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> </span>
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630
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<pre style="margin: 0;">+<span id="LC630" 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;">cutLen_read</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">min_readLen</span><span class="p">){</span></span>
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<td class="diff-line-num 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 class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<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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<pre style="margin: 0;">+<span id="LC632" 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;">Option post-trim-length omitted, as it is shorter than min read length.</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>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="c"> <span class="p">}</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="c"> </span>
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599
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"> </span>
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600
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// quality-based trimming</span></span>
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601
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637
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<pre style="margin: 0;"> <span id="LC637" 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">@@ -624,7 +660,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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624
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<pre style="margin: 0;"> <span id="LC660" 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;">"qtrim-format: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">quality</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="c"> <span class="p">}</span></span>
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626
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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627
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<pre style="margin: 0;">-<span id="LC627" 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 class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Specify qtrim-format for quality-based trimming.</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>
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663
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<pre style="margin: 0;">+<span id="LC663" 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;">"Specify qtrim-format for quality-based trimming.</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>
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"> <span class="p">}</span></span>
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666
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<pre style="margin: 0;"> <span id="LC666" 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">@@ -658,6 +694,42 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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658
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="c"> <span class="p">}</span></span>
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695
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// trimming of homopolymers</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC699" 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;">"htrim-left"</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;">"htrim-right"</span><span class="p">)){</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="c"> </span>
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701
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<pre style="margin: 0;">+<span id="LC701" 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;">"htrim-left"</span><span class="p">)){</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" 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;">htrimLeft</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-left"</span><span class="p">);</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" 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;">"htrim-left: "</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;">htrimLeft</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> </span>
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706
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<pre style="margin: 0;">+<span id="LC706" 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;">"htrim-right"</span><span class="p">)){</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" 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;">htrimRight</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-right"</span><span class="p">);</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" 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;">"htrim-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;">htrimRight</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="c"> <span class="p">}</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c"> </span>
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<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
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<pre style="margin: 0;">+<span id="LC711" 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;">"htrim-max-length"</span><span class="p">)){</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" 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;">htrimMaxLength</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-max-length"</span><span class="p">);</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC713" 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;">"htrim-max-length: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMaxLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="c"> </span>
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715
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<pre style="margin: 0;">+<span id="LC715" 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;">"htrim-max-first"</span><span class="p">)){</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC716" 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;">"htrim-max-first: on"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new 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
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMaxFirstOnly</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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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="c"> <span class="p">}</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="c"> <span class="p">}</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="c"> </span>
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<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
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<pre style="margin: 0;">+<span id="LC721" 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;">htrimMinLength</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-min-length"</span><span class="p">);</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC722" 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;">"htrim-min-length: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMinLength</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="c"> </span>
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<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
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<pre style="margin: 0;">+<span id="LC724" 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;">h_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"htrim-error-rate"</span><span class="p">);</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC725" 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;">"htrim-error-rate: "</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;">h_errorRate</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="c"> </span>
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727
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<pre style="margin: 0;">+<span id="LC727" 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;">"htrim-adapter"</span><span class="p">)){</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" 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;">"htrim-adapter: on"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new 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
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimAdapterRm</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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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="c"> <span class="p">}</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="c"> <span class="p">}</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="c"> </span>
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661
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// output, logging and tagging options</span></span>
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="c"> </span>
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663
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735
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<pre style="margin: 0;"> <span id="LC735" 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;">"align-log"</span><span class="p">)){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -692,7 +764,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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692
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"length-dist"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeLengthDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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693
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"number-tags"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useNumberTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
694
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"removal-tags"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useRemovalTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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695
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"umi-tags"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">randTag</span></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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767
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<pre style="margin: 0;">+<span id="LC767" 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;">"umi-tags"</span><span class="p">))</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">umiTags</span></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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696
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="c"> </span>
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697
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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698
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); 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="782" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -710,7 +782,7 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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710
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782
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<pre style="margin: 0;"> <span id="LC782" 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;">b_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">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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<td class="diff-line-num old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
711
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<td class="diff-line-num new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
783
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<pre style="margin: 0;"> <span id="LC783" 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;">b_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_end</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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<td class="diff-line-num old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
712
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<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
713
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<td class="diff-line-num new_line old" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); 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 noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC713" 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 class="idiff left right">Specified barcode trim-end is unknown!</span></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>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
785
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC785" 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;"><span class="idiff left">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">Specified barcode trim-end is unknown.</span></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>
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<td class="diff-line-num old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
714
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<td class="diff-line-num new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
786
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC786" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
715
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<td class="diff-line-num new_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
716
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<td class="diff-line-num new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-trim-end: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b_trim_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -724,6 +796,11 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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724
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<td class="diff-line-num new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isSet</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-min-overlap"</span><span class="p">)){</span></span>
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<td class="diff-line-num old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
725
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<td class="diff-line-num new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-min-overlap"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
726
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<td class="diff-line-num new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
798
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC798" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"barcode-min-overlap: "</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_min_overlap</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="c"> </span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<td class="diff-line-num new old_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">
</td>
<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="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;">Barcode min-overlap should be 1 at least.</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>
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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
727
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<td class="diff-line-num new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
804
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC804" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
728
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<td class="diff-line-num new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
729
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<td class="diff-line-num new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"barcode-error-rate"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -763,13 +840,13 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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763
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<td class="diff-line-num new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a_trim_end</span><span class="p">;</span></span>
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-trim-end"</span><span class="p">);</span></span>
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765
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="c"> </span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LEFT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">;</span></span>
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768
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<td class="diff-line-num new_line old" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ANY"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">;</span></span>
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769
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<td class="diff-line-num new_line old" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">;</span></span>
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770
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<td class="diff-line-num new_line old" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">;</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LEFT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">a_</span>end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">a_</span>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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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ANY"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">a_</span>end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">a_</span>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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<td class="diff-line-num new new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">a_</span>end</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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771
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<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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772
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<td class="diff-line-num new_line old" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right">Specified adapter trim-end is unknown!</span></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>
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<td class="diff-line-num new old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
849
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<pre style="margin: 0;">+<span id="LC849" 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;"><span class="idiff left">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">Specified adapter trim-end is unknown.</span></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>
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773
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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774
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="c"> <span class="p">}</span></span>
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775
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<td class="diff-line-num new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
852
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<pre style="margin: 0;"> <span id="LC852" 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-trim-end: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">a_trim_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -781,12 +858,38 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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781
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="c"> <span class="p">}</span></span>
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782
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="c"> </span>
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783
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860
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<pre style="margin: 0;"> <span id="LC860" 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-revcomp"</span><span class="p">)){</span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" 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-revcomp: yes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">revCompAdapter</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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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="c"> </span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">rcModeStr</span><span class="p">;</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">rcModeStr</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>
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864
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<pre style="margin: 0;">+<span id="LC864" 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-revcomp: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rcModeStr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"> </span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rcModeStr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ON"</span><span class="p">)</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="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" 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;">rcModeStr</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;">rcMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RCONLY</span><span class="p">;</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="c"> </span>
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869
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<pre style="margin: 0;">+<span id="LC869" 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-revcomp-end"</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;">rcMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RCON</span><span class="p">){</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> </span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">arc_trim_end</span><span class="p">;</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">getOptionValue</span><span class="p">(</span><span class="n" style="color: #333;">arc_trim_end</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-revcomp-end"</span><span class="p">);</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"> </span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">arc_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LEFT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">arc_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" 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;">arc_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RIGHT"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">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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<td class="diff-line-num new new_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
876
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<pre style="margin: 0;">+<span id="LC876" 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;">arc_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ANY"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">arc_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
877
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<pre style="margin: 0;">+<span id="LC877" 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;">arc_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"LTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">arc_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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<td class="diff-line-num new new_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
878
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<pre style="margin: 0;">+<span id="LC878" 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;">arc_trim_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"RTAIL"</span><span class="p">)</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">arc_end</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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<td class="diff-line-num new new_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
879
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<pre style="margin: 0;">+<span id="LC879" 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 new_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
880
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<pre style="margin: 0;">+<span id="LC880" 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;">Specified reverse complement adapter trim-end is unknown.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
884
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<pre style="margin: 0;">+<span id="LC884" 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;">arc_end</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="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
885
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<pre style="margin: 0;">+<span id="LC885" 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-revcomp-end: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arc_trim_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useRcTrimEnd</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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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="c"> <span class="p">}</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="c"> <span class="p">}</span></span>
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786
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="c"> <span class="p">}</span></span>
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787
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890
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="c"> </span>
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788
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891
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<pre style="margin: 0;"> <span id="LC891" 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-relaxed"</span><span class="p">)){</span></span>
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789
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<td class="diff-line-num new_line old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC789" 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-relaxed: <span class="idiff left right">yes</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" 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-relaxed: <span class="idiff left right">on</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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790
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<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
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<pre style="margin: 0;"> <span id="LC893" 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>
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791
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="c"> <span class="p">}</span></span>
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792
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -802,6 +905,11 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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802
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<td class="diff-line-num new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
905
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<pre style="margin: 0;"> <span id="LC905" 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;">a_min_overlap</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-overlap"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
803
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<td class="diff-line-num new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
906
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<pre style="margin: 0;"> <span id="LC906" 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-min-overlap: "</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_min_overlap</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
804
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
908
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<pre style="margin: 0;">+<span id="LC908" 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;">a_min_overlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<td class="diff-line-num new old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
909
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<pre style="margin: 0;">+<span id="LC909" 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;">Adapter min-overlap should be 1 at least.</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>
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<td class="diff-line-num new new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="c"> <span class="p">}</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="c"> </span>
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805
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<td class="diff-line-num new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
913
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<pre style="margin: 0;"> <span id="LC913" 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;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter-error-rate"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
806
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<td class="diff-line-num new_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="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-error-rate: "</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_errorRate</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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807
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<td class="diff-line-num new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); 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="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -810,6 +918,14 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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810
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<td class="diff-line-num new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
811
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<td class="diff-line-num new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
919
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<pre style="margin: 0;"> <span id="LC919" class="line" lang="c"> <span class="p">}</span></span>
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812
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" 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;">a_cycles</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>
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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" 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;">a_cycles</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;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"adapter-cycles: "</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_cycles</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
924
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<pre style="margin: 0;">+<span id="LC924" 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;">a_cycles</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" 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;">Number of adapter removal cycles should be 1 at least.</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>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="c"> <span class="p">}</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="c"> </span>
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813
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// getOptionValue(o.a_overhang, parser, "adapter-overhang");</span></span>
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814
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// *out << "adapter-overhang: " << o.a_overhang << endl;</span></span>
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815
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); 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="946" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -830,14 +946,6 @@ void loadOptions(Options &o, seqan::ArgumentParser &parser){</td>
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830
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</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="n" style="color: #333;">endl</span><span class="p">;</span></span>
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831
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="c"> <span class="p">}</span></span>
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832
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="c"> </span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="c"> </span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// option compatibility tests</span></span>
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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="c"> </span>
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836
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<pre style="margin: 0;">-<span id="LC836" 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;">cutLen_read</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">min_readLen</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
837
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<td class="diff-line-num new_line old" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">cutLen_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
838
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<pre style="margin: 0;">-<span id="LC838" 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;">Option post-trim-length omitted, as it is shorter than min read length.</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>
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839
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="c"> <span class="p">}</span></span>
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840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="c"> </span>
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841
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="c"><span class="p">}</span></span>
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842
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950
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="c"></span>
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843
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951
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="c"></span>
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<li id="39ce06c130af5661718537ce52c57783c42daa69">
<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#39ce06c130af5661718537ce52c57783c42daa69"><strong>src/PairedAlign.h</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,12 +12,22 @@ class PairedAlign : public tbb::filter {</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"> </span>
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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;">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>
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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;">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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<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_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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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">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="LC19" class="line" lang="c"> </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_htrimMinLength</span><span class="p">,</span> <span class="n" style="color: #333;">m_htrimMaxLength</span><span class="p">;</span></span>
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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;">float</span> <span class="n" style="color: #333;">m_htrimErrorRate</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="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_arTimes</span><span class="p">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC25" 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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17
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26
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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;">LogAlign</span> <span class="n" style="color: #333;">m_log</span><span class="p">;</span></span>
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18
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27
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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;">RunType</span> <span class="n" style="color: #333;">m_runType</span><span class="p">;</span></span>
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28
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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;">BarcodeDetect</span> <span class="n" style="color: #333;">m_barType</span><span class="p">;</span></span>
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29
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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;">AdapterRemoval</span> <span class="n" style="color: #333;">m_adapRem</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TrimEnd</span> <span class="n" style="color: #333;">m_aTrimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">m_arcTrimEnd</span><span class="p">,</span> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC32" 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_unassigned</span><span class="p">;</span></span>
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23
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33
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<pre style="margin: 0;"> <span id="LC33" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m_adapters</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m_adapters2</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">@@ -33,11 +43,26 @@ public:</td>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">PairedAlign</span><span class="p">(</span><span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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34
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> </span>
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35
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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">
45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">filter</span><span class="p">(</span><span class="n" style="color: #333;">parallel</span><span class="p">),</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" 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>
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36
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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">
47
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<pre style="margin: 0;"> <span id="LC47" 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>
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37
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">m_runType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">runType</span><span class="p">),</span></span>
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38
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">m_barType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span><span class="p">),</span></span>
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39
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">m_adapRem</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">adapRm</span><span class="p">),</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">m_aTrimEnd</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_end</span><span class="p">),</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">m_arcTrimEnd</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">arc_end</span><span class="p">),</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">m_bTrimEnd</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_end</span><span class="p">),</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">m_arTimes</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_cycles</span><span class="p">),</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" 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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<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="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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40
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57
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<pre style="margin: 0;"> <span id="LC57" 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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58
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<pre style="margin: 0;">+<span id="LC58" 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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59
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<pre style="margin: 0;">+<span id="LC59" 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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60
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<pre style="margin: 0;">+<span id="LC60" 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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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">m_htrimMaxLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMaxLength</span><span class="p">),</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">m_htrimMaxFirstOnly</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimMaxFirstOnly</span><span class="p">),</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">m_htrimErrorRate</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">h_errorRate</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_htrimAdapterRm</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimAdapterRm</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_htrim</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="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">htrimRight</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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41
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span> <span class="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;">WITHIN_READ_REMOVAL2</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;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">WITHIN_READ2</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">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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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">m_unassigned</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,11 +72,11 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">m_barcodes2</span> <span class="o" style="font-weight: 600;">=</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;">barcodes2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">m_adapters2</span> <span class="o" style="font-weight: 600;">=</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;">adapters2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> </span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">m_b1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_adapters</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_tail_len</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">m_b1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_barcodes</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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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="c"> <span class="n" style="color: #333;">m_a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_adapters</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_tail_len</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">m_b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_barcodes2</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">m_a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_adapters2</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_tail_len</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">false</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;">m_b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_barcodes2</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">b_gapCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">m_a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqAlign</span><span class="p">(</span><span class="n" style="color: #333;">m_adapters2</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_min_overlap</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_tail_len</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_log</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;">TAB</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" 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;">"ReadTag</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QueryTag</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QueryStart</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QueryEnd</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">OverlapLength</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Mismatches</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Indels</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AllowedErrors"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,18 +91,18 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">Barcode</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TPairedRead</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pRead</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TAlignBundle</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">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">ComputeCycle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">idxAl</span></span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">ToBarcodes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TPairedRead</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pRead</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TAlignBundle</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">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">ComputeCycle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">idxAl</span></span><span class="p"><span class="idiff">,</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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">AlignmentMode</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">alMode</span></span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC96" 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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97
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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;">m_barType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BOFF</span><span class="p">){</span></span>
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74
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> </span>
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75
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100
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<pre style="margin: 0;"> <span id="LC100" 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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76
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<pre style="margin: 0;">-<span id="LC76" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC77" 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>
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<pre style="margin: 0;">-<span id="LC78" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" 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>
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80
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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC80" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<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">
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<pre style="margin: 0;">+<span id="LC101" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_bTrimEnd</span></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="LC102" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_bTrimEnd</span></span><span class="p">);</span></span>
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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="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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_bTrimEnd</span></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 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="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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_bTrimEnd</span></span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_bTrimEnd</span></span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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81
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106
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<pre style="margin: 0;"> <span id="LC106" 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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82
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"> <span class="p">}</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" 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">@@ -89,18 +114,113 @@ public:</td>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> </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="LC92" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">Adapter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TPairedRead</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pRead</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TAlignBundle</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">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">ComputeCycle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">idxAl</span></span><span class="p">){</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">ToAdapters</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TPairedRead</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pRead</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TAlignBundle</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">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">ComputeCycle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">idxAl</span></span><span class="p"><span class="idiff">,</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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">AlignmentMode</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">alMode</span></span><span class="p"><span class="idiff">,</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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TrimEnd</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimEnd</span></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="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="LC120" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC121" 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;">AOFF</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC123" 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="LC99" 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>
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<pre style="margin: 0;">+<span id="LC124" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alMode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimEnd</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC126" 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>
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<pre style="margin: 0;">-<span id="LC102" 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>
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<pre style="margin: 0;">-<span id="LC103" 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>
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<pre style="margin: 0;">+<span id="LC127" 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>
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<pre style="margin: 0;">+<span id="LC128" 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>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="p">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="p">}</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimLeftHPS</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> </span>
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136
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<pre style="margin: 0;">+<span id="LC136" 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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<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="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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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> </span>
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139
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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_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">){</span></span>
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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;">seqRead</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="p">(</span><span class="n" style="color: #333;">m_aTrimEnd</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;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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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="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;">seqRead</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="p">(</span><span class="n" style="color: #333;">m_arcTrimEnd</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;">m_arcTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" 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_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">){</span></span>
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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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_aTrimEnd</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;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="p">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> </span>
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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">
147
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<pre style="margin: 0;">+<span id="LC147" 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_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">seqRead</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;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rmAdapterRC</span><span class="p">){</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> </span>
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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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_htrimLeft</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> </span>
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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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_htrimLeft</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> </span>
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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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> </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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> </span>
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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">
158
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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;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>
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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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="p">}</span></span>
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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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_htrimErrorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)){</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> </span>
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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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrimMaxLength</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m_htrimMaxLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_htrimMaxFirstOnly</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="p">}</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_htrimMinLength</span><span class="p">){</span></span>
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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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> </span>
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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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>
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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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="p">}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="p">}</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> </span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> </span>
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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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimRightHPS</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> </span>
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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">
183
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<pre style="margin: 0;">+<span id="LC183" 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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<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">
184
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<pre style="margin: 0;">+<span id="LC184" 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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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> </span>
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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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">){</span></span>
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<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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rmAdapter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LEFT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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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="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;">seqRead</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="p">(</span><span class="n" style="color: #333;">m_arcTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LEFT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_arcTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<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="c"> <span class="p">}</span></span>
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<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="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_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_useRcTrimEnd</span><span class="p">){</span></span>
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<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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LEFT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_aTrimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LTAIL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="p">}</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> </span>
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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="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_htrimAdapterRm</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">seqRead</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;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rmAdapterRC</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_htrimRight</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> </span>
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<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="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_htrimRight</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> </span>
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200
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<pre style="margin: 0;">+<span id="LC200" 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;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<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="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqLen</span><span class="p">;</span></span>
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<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="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> </span>
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<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="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<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="c"> </span>
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<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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>
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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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="p">}</span></span>
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<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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_htrimErrorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">seqLen</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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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"> </span>
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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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrimMaxLength</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">m_htrimMaxLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_htrimMaxFirstOnly</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="p">}</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"> </span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">m_htrimMinLength</span><span class="p">){</span></span>
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<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">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">));</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"> </span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">));</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="c"> <span class="p">}</span></span>
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104
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <span class="p">}</span></span>
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105
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="p">}</span></span>
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226
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<pre style="margin: 0;"> <span id="LC226" 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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,6 +235,17 @@ public:</td>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"> </span>
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116
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">TPairedReadBundle</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prBundle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TPairedReadBundle</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">);</span></span>
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117
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c"> </span>
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238
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<pre style="margin: 0;">+<span id="LC238" 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="p">){</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">prBundle</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="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>
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241
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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 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="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="p">)</span></span>
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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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">prBundle</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="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>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c"> <span class="p">}</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="p">}</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c"> </span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">AlignmentMode</span> <span class="n" style="color: #333;">alMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALIGNALL</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c"> </span>
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118
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// barcode detection</span></span>
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119
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> </span>
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120
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_barType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BOFF</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -135,7 +266,7 @@ public:</td>
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135
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="p">}</span></span>
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136
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> </span>
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137
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268
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<pre style="margin: 0;"> <span id="LC268" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<td class="diff-line-num new_line old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">Barcode</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prBundle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">idxAl</span></span><span class="p">);</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">ToBarcodes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prBundle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">idxAl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alMode</span></span><span class="p">);</span></span>
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139
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="p">}</span></span>
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140
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"> </span>
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141
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<pre style="margin: 0;"> <span id="LC272" 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="mi" style="color: #099;">3</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,7 +275,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> </span>
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146
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277
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<pre style="margin: 0;"> <span id="LC277" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">Barcode</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prBundle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">idxAl</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedRead<span class="idiff left">ToBarcodes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prBundle</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alBundle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">idxAl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alMode</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="p">}</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -152,31 +283,86 @@ public:</td>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> </span>
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284
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<pre style="margin: 0;"> <span id="LC284" 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;">AOFF</span><span class="p">){</span></span>
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154
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">TAlignBundle</span> <span class="n" style="color: #333;">alBundle</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">Alignments</span> <span class="n" style="color: #333;">r1AlignmentsA</span><span class="p">,</span> <span class="n" style="color: #333;">r2AlignmentsA</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>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">alBundle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">r1AlignmentsA</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">alBundle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">r2AlignmentsA</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">idxAl</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c"> </span>
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164
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<pre style="margin: 0;">-<span id="LC164" 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="mi" style="color: #099;">2</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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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">idxAl</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">cycle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">PRELOAD</span><span class="p">);</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" 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;">c</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;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_arTimes</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c</span><span class="p">){</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c"> <span class="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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_aTrimEnd</span><span class="p">;</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c"> <span class="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;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c"> </span>
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292
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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;">m_useRcTrimEnd</span><span class="p">){</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <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="p">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c"> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> </span>
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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">
297
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<pre style="margin: 0;">+<span id="LC297" 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;">r</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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">r</span><span class="p">){</span></span>
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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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useRcTrimEnd</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c"> <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="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">trimEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_arcTrimEnd</span><span class="p">;</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="p">}</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> </span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="n" style="color: #333;">TAlignBundle</span> <span class="n" style="color: #333;">alBundle</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">Alignments</span> <span class="n" style="color: #333;">r1AlignmentsA</span><span class="p">,</span> <span class="n" style="color: #333;">r2AlignmentsA</span><span class="p">;</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> </span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="n" style="color: #333;">alBundle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">r1AlignmentsA</span><span class="p">);</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">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">alBundle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">r2AlignmentsA</span><span class="p">);</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> </span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">idxAl</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> </span>
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313
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<pre style="margin: 0;">+<span id="LC313" 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="mi" style="color: #099;">2</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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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="n" style="color: #333;">idxAl</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">cycle</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">PRELOAD</span><span class="p">);</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c"> <span class="p">}</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"> </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="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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<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="c"> <span class="n" style="color: #333;">alignPairedReadToAdapters</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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;">alBundle</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="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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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"> <span class="p">}</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"> </span>
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322
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<pre style="margin: 0;">+<span id="LC322" 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="mi" style="color: #099;">2</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="LC323" class="line" lang="c"> <span class="n" style="color: #333;">idxAl</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="c"> <span class="n" style="color: #333;">cycle</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;">COMPUTE</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"> <span class="p">}</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="c"> </span>
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327
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<pre style="margin: 0;">+<span id="LC327" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedReadToAdapters</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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;">alBundle</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="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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="c"> <span class="p">}</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c"> <span class="p">}</span></span>
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167
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> </span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> <span class="p">}</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="c"> </span>
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334
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<pre style="margin: 0;">+<span id="LC334" 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="p">){</span></span>
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169
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335
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<pre style="margin: 0;"> <span id="LC335" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedReadAdapter</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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;">alBundle</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="p">);</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c"> </span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="c"> </span>
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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">
339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="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="p">){</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">prBundle</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="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>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="c"> </span>
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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">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">prBundle</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="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>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="c"> <span class="p">}</span></span>
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171
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> <span class="p">}</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> </span>
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173
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<pre style="margin: 0;">-<span id="LC173" 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="mi" style="color: #099;">2</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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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">idxAl</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">cycle</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;">COMPUTE</span><span class="p">;</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="c"> <span class="p">}</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="c"> </span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrim</span><span class="p">){</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrimLeft</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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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="c"> <span class="n" style="color: #333;">trimLeftHPS</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="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="p">)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="c"> <span class="n" style="color: #333;">trimLeftHPS</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="c"> <span class="p">}</span></span>
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176
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"> <span class="p">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> </span>
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178
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<pre style="margin: 0;">-<span id="LC178" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">alignPairedReadAdapter</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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;">alBundle</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="p">);</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_htrimRight</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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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="c"> </span>
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360
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<pre style="margin: 0;">+<span id="LC360" 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;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="c"> <span class="n" style="color: #333;">trimRightHPS</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c"> </span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="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="p">)</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">trimRightHPS</span><span class="p">(</span><span class="n" style="color: #333;">prBundle</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="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="LC365" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="c"> <span class="p">}</span></span>
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182
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="c"> </span>
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<li id="35b9932b85a450e1d8d94d54dc291117458373e3">
<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#35b9932b85a450e1d8d94d54dc291117458373e3"><strong>src/PairedInput.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">@@ -12,7 +12,7 @@ class PairedInput : public tbb::filter {</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"> </span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" 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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15
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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;">bool</span> <span class="n" style="color: #333;">m_isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">m_useBarRead</span><span class="p">,</span> <span class="n" style="color: #333;">m_useNumberTag</span><span class="p">;</span></span>
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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;">bool</span> <span class="n" style="color: #333;">m_isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">m_useBarRead</span><span class="p">,</span> <span class="n" style="color: #333;">m_useNumberTag</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_interleaved</span></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="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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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> </span>
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18
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<pre style="margin: 0;"> <span id="LC18" 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_uncalled</span><span class="p">,</span> <span class="n" style="color: #333;">m_uncalledPairs</span><span class="p">,</span> <span class="n" style="color: #333;">m_tagCounter</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">@@ -25,6 +25,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;">filter</span><span class="p">(</span><span class="n" style="color: #333;">serial_in_order</span><span class="p">),</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" 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>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="n" style="color: #333;">m_useNumberTag</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">useNumberTag</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">m_interleaved</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">interleavedInput</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC29" 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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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">m_useBarRead</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span> <span class="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;">BARCODE_READ</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC31" 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>
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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">@@ -37,7 +38,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">m_f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">m_b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="idiff left"> </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">m_interleaved</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">m_f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">SeqInput</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="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">readsFile2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</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="LC43" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</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">@@ -61,9 +62,17 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">TStrings</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">quals2</span><span class="p">,</span> <span class="n" style="color: #333;">qualsBR</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;">TBools</span> <span class="n" style="color: #333;">uncalled</span><span class="p">,</span> <span class="n" style="color: #333;">uncalled2</span><span class="p">,</span> <span class="n" style="color: #333;">uncalledBR</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC64" 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;">nReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loadSeqReads</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</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;">m_bundleSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" 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;">bundleSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_bundleSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_interleaved</span><span class="p">)</span> <span class="n" style="color: #333;">bundleSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_bundleSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC68" 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;">nReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loadSeqReads</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</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;">bundleSize</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_interleaved</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nReads</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC71" 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;">ERROR: Interleaved reads input does not contain even number of reads.</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>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_interleaved</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC76" 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;">nReads2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loadSeqReads</span><span class="p">(</span><span class="n" style="color: #333;">uncalled2</span><span class="p">,</span> <span class="n" style="color: #333;">ids2</span><span class="p">,</span> <span class="n" style="color: #333;">seqs2</span><span class="p">,</span> <span class="n" style="color: #333;">quals2</span><span class="p">,</span> <span class="n" style="color: #333;">m_bundleSize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nReads</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nReads2</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">@@ -75,11 +84,14 @@ public:</td>
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75
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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">){</span></span>
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76
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" 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;">nBarReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loadSeqReads</span><span class="p">(</span><span class="n" style="color: #333;">uncalledBR</span><span class="p">,</span> <span class="n" style="color: #333;">idsBR</span><span class="p">,</span> <span class="n" style="color: #333;">seqsBR</span><span class="p">,</span> <span class="n" style="color: #333;">qualsBR</span><span class="p">,</span> <span class="n" style="color: #333;">m_bundleSize</span><span class="p">);</span></span>
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77
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> </span>
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78
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<td class="diff-line-num new_line old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nReads</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nBarReads</span><span class="p">){</span></span>
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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">
87
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<pre style="margin: 0;">+<span id="LC87" 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;">multi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num 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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_interleaved</span><span class="p">)</span> <span class="n" style="color: #333;">multi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> </span>
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<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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nReads</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nBarReads</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">multi</span><span class="p">){</span></span>
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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
79
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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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<pre style="margin: 0;"> <span id="LC91" 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;">ERROR: Read without barcode read in input.</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>
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80
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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81
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="p">}</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" 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;">nReads</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nBarReads</span><span class="p">){</span></span>
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<td class="diff-line-num new old_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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<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="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;">nReads</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nBarReads</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">multi</span></span><span class="p">){</span></span>
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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
83
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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
95
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<pre style="margin: 0;"> <span id="LC95" 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;">ERROR: Barcode read without read in input.</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>
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84
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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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85
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97
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<pre style="margin: 0;"> <span id="LC97" 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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,44 +102,96 @@ public:</td>
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90
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> </span>
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91
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">TPairedReadBundle</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prBundle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TPairedReadBundle</span><span class="p">();</span></span>
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92
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</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">length</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ids</span></span><span class="p"><span class="idiff">);</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">){</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_interleaved</span></span><span class="p">){</span></span>
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94
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> </span>
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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;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">uncalled2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])){</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> </span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</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;">m_uncalled</span><span class="p">;</span></span>
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98
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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;">m_isPaired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">uncalled2</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;">m_uncalled</span><span class="p">;</span></span>
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99
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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;">m_isPaired</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_uncalledPairs</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="p">}</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// else if(m_useBarRead && uncalledBR[i]){</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// // to be handled</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" 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>
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106
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"> </span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useNumberTag</span><span class="p">){</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">converter</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">converter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_tagCounter</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">tagCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">converter</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">uncalled2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])){</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</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;">m_uncalled</span><span class="p">;</span></span>
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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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">uncalled2</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;">m_uncalled</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_uncalledPairs</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="p">}</span></span>
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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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// else if(m_useBarRead && uncalledBR[i]){</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// // to be handled</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useNumberTag</span><span class="p">){</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">converter</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">converter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_tagCounter</span><span class="p">;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">tagCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">converter</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> </span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">ids</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;">tagCount</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">ids2</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;">tagCount</span><span class="p">;</span></span>
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128
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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_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">idsBR</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;">tagCount</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="p">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">TSeqRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> </span>
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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_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTA</span><span class="p">){</span></span>
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<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;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids</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 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 class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids2</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 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_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</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 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="p">}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" 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 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="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">quals</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 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;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">quals2</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 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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">qualsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="p">}</span></span>
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111
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> </span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">ids</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;">tagCount</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">ids2</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;">tagCount</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">idsBR</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;">tagCount</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TPairedRead</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">barRead</span><span class="p">));</span></span>
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115
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="p">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="p">}</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="p">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// interleaved paired input</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> </span>
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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">
150
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<pre style="margin: 0;">+<span id="LC150" 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;">nEntries</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</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="mi" style="color: #099;">2</span><span class="p">);</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> </span>
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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">
152
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<pre style="margin: 0;">+<span id="LC152" 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;">nEntries</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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116
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> </span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">TSeqRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" 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;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" 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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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118
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> </span>
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119
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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_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTA</span><span class="p">){</span></span>
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120
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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</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 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]){</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> </span>
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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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">])</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_uncalled</span><span class="p">;</span></span>
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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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">uncalled</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_uncalled</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_uncalledPairs</span><span class="p">;</span></span>
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123
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// else if(m_useBarRead && uncalledBR[i]){</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// // to be handled</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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124
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">ids2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">quals2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">qualsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> </span>
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170
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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_useNumberTag</span><span class="p">){</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">converter</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">converter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m_tagCounter</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">TString</span> <span class="n" style="color: #333;">tagCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">converter</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> </span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tagCount</span><span class="p">;</span></span>
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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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tagCount</span><span class="p">;</span></span>
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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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">idsBR</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;">tagCount</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> </span>
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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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">TSeqRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="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>
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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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]);</span></span>
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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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</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 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="p">}</span></span>
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<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">
187
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<pre style="margin: 0;">+<span id="LC187" 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 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="c"> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">],</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">]);</span></span>
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<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="c"> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">],</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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<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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_useBarRead</span><span class="p">)</span> <span class="n" style="color: #333;">barRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TSeqRead</span><span class="p">(</span><span class="n" style="color: #333;">seqsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">idsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">qualsBR</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> </span>
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<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="c"> <span class="n" style="color: #333;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TPairedRead</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">barRead</span><span class="p">));</span></span>
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128
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="p">}</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> </span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">prBundle</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">TPairedRead</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">barRead</span><span class="p">));</span></span>
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131
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="p">}</span></span>
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132
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC197" 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">@@ -176,20 +240,20 @@ public:</td>
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"> </span>
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"> </span>
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178
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">();</span></span>
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<td class="diff-line-num new old_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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<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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="idiff left"> </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">m_interleaved</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">();</span></span>
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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="c"> <span class="k" style="font-weight: 600;">else</span> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedReads</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); 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="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">();</span></span>
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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">
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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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="idiff left"> </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">m_interleaved</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrProcessedChars</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_isPaired</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">();</span></span>
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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;">m_isPaired</span><span class="idiff left"> </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">m_interleaved</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">m_f2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNrLowPhredReads</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC257" 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>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#5892684acbf66442a550859d89842772d4e04d36"><strong>src/PairedOutput.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">@@ -16,15 +16,11 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_mapsize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimThresh</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimWinSize</span><span class="p">;</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_isPaired</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeUnassigned</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">m_writeSingleReadsP</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m_randTag</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_twoBarcodes</span><span class="p">,</span> <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="n" style="color: #333;">tbb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m_nSingleReads</span><span class="p">,</span> <span class="n" style="color: #333;">m_nLowPhred</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">m_target</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">,</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">m_errorRate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC25" 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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30
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,16 +46,11 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">m_runType</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">runType</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">m_barDetect</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">barDetect</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">m_minLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">min_readLen</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimLeftNucs</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">trimRightNucs</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">hpsMinLength</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">m_errorRate</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">a_errorRate</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">m_qtrim</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">qTrim</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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="LC51" 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="LC52" 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="LC53" 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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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">m_randTag</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC54" 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="LC55" 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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65
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">m_writeSingleReadsP</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">writeSingleReadsP</span><span class="p">),</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -235,72 +226,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_trimLeftNucs</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_errorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)){</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="p">}</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="p">}</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c"> </span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"> </span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">);</span></span>
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265
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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="p">}</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c"> <span class="p">}</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c"> </span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"> </span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TSeqRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqRead</span><span class="p">){</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c"> </span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c"> </span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">nuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_trimRightNucs</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">];</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c"> </span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<td class="diff-line-num new_line old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nuc</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
286
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<td class="diff-line-num new_line old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">notNuc</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">notNuc</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m_errorRate</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">)){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="c"> <span class="p">}</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="c"> <span class="p">}</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cutPos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">m_hpsMinLength</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">));</span></span>
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295
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<td class="diff-line-num new_line old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
297
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<td class="diff-line-num new_line old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">cutPos</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writePairedRead</span><span class="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TPairedRead</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pRead</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">flexbar</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -319,11 +244,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC244" 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="LC245" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimLeftNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimRightNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_randTag</span><span class="p">)</span> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC247" 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="LC248" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="n" style="color: #333;">m_outMap</span><span class="p">[</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">barID</span><span class="p">].</span><span class="n" style="color: #333;">f1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writeRead</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -355,23 +275,6 @@ public:</td>
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355
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<pre style="margin: 0;"> <span id="LC275" 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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356
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="p">}</span></span>
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357
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> </span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimLeftNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="c"> <span class="n" style="color: #333;">trimLeftNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c"> <span class="p">}</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_trimRightNucs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="c"> <span class="n" style="color: #333;">trimRightNucs</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="c"> <span class="p">}</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="c"> </span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_randTag</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> </span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">)</span> <span class="n" style="color: #333;">l1ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">pRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">m_minLength</span><span class="p">)</span> <span class="n" style="color: #333;">l2ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#2d8e74575f3f55a6c54f0d5fb8616a4f679c16fd"><strong>src/SeqAlign.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">@@ -11,11 +11,10 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">AlignResults</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TSeqStr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TAlignResults</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="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;">m_trimEnd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" 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;">LogAlign</span> <span class="n" style="color: #333;">m_log</span><span class="p">;</span></span>
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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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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_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_<span class="idiff left right">randTag</span></span><span class="p">,</span> <span class="n" style="color: #333;">m_strictRegion</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_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_<span class="idiff left right">umiTags</span></span><span class="p">,</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="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="LC19" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">m_errorRate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,14 +28,13 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">SeqAlign</span><span class="p">(</span><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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minOverlap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">errorRate</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailLength</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapCost</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TrimEnd</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBarcoding</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">SeqAlign</span><span class="p">(</span><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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">queries</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minOverlap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">errorRate</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tailLength</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapCost</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;">isBarcoding</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">m_minOverlap</span><span class="p">(</span><span class="n" style="color: #333;">minOverlap</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_errorRate</span><span class="p">(</span><span class="n" style="color: #333;">errorRate</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_tailLength</span><span class="p">(</span><span class="n" style="color: #333;">tailLength</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">m_trimEnd</span><span class="p">(</span><span class="n" style="color: #333;">end</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_isBarcoding</span><span class="p">(</span><span class="n" style="color: #333;">isBarcoding</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">m_<span class="idiff left">randTag</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">randTag</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">m_<span class="idiff left">umiTags</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">o</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">umiTags</span></span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">m_minLength</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">min_readLen</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC39" 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>
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<pre style="margin: 0;"> <span id="LC40" 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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,14 +44,14 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC44" 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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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">m_nPreShortReads</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">m_modified</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">algo</span><span class="p">(</span><span class="n" style="color: #333;">TAlgorithm</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">end</span></span><span class="p">)){</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">algo</span><span class="p">(</span><span class="n" style="color: #333;">TAlgorithm</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">gapCost</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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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">m_queries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queries</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">m_rmOverlaps</span> <span class="o" style="font-weight: 600;">=</span> <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="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="p">(</span><span class="n" style="color: #333;">flexbar</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MAX_READLENGTH</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC53" 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>
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<pre style="margin: 0;">+<span id="LC54" 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 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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">AlignmentMode</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">alMode</span></span><span class="p"><span class="idiff">,</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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TrimEnd</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimEnd</span></span><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 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="LC57" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,16 +76,19 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="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;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC78" 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;">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="LC80" 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="LC81" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC82" 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;">qseq</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;">seq</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;">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>
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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="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">m_trimEnd</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">LTAIL</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">m_</span>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="LC86" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">trimEnd</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">LTAIL</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;">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="LC87" 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="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="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>
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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="n" style="color: #333;"><span class="idiff left right">m_</span>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>
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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="idiff left right"> </span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suffix</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;">readLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tailLength</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" 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>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suffix</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;">readLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tailLength</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;">rseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"> <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">@@ -112,10 +113,13 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// align each query sequence and store best one</span></span>
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<pre style="margin: 0;"> <span id="LC114" 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;">m_queries</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC116" 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="LC117" 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="LC118" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">TAlignResults</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// global sequence alignment</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimEnd</span></span><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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<pre style="margin: 0;"> <span id="LC124" 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>
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<pre style="margin: 0;"> <span id="LC125" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,8 +132,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">validAl</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="LC134" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(((</span><span class="n" style="color: #333;"><span class="idiff left">m_trimEnd</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">RTAIL</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">m_</span>trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">)</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;">startPosA</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;">startPosS</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">m_trimEnd</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">LTAIL</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">m_</span>trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LEFT</span><span class="p">)</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;">endPosA</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;">endPosS</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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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="n" style="color: #333;"><span class="idiff left">trimEnd</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">RTAIL</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;">trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RIGHT</span><span class="p">)</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;">startPosA</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;">startPosS</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">trimEnd</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">LTAIL</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;">trimEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LEFT</span><span class="p">)</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;">endPosA</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;">endPosS</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m_strictRegion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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133
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137
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<pre style="margin: 0;"> <span id="LC137" 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="mi" style="color: #099;">1</span><span class="p">){</span></span>
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134
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> </span>
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135
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">validAl</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="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>
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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">@@ -149,24 +153,24 @@ public:</td>
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149
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// valid alignment</span></span>
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150
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qIndex</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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151
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> </span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">TrimEnd</span> <span class="n" style="color: #333;">tr<span class="idiff left">imEnd</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">m_</span>trimEnd</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">TrimEnd</span> <span class="n" style="color: #333;">tr<span class="idiff left">End</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;">trimEnd</span><span class="p">;</span></span>
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153
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> </span>
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154
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// trim read based on alignment</span></span>
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155
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">performRemoval</span><span class="p">){</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"> </span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tr<span class="idiff left right">im</span>End</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ANY</span><span class="p">){</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">trEnd</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ANY</span><span class="p">){</span></span>
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158
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"> </span>
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159
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">startPosA</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">startPosS</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">endPosS</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">endPosA</span><span class="p">){</span></span>
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160
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">seq</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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161
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">)</span> <span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="p">}</span></span>
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163
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167
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<pre style="margin: 0;"> <span id="LC167" 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;">am</span><span class="p">.</span><span class="n" style="color: #333;">startPosA</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">startPosS</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">endPosS</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;">endPosA</span><span class="p">){</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">tr<span class="idiff left right">im</span>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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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">trEnd</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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165
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="p">}</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">tr<span class="idiff left right">im</span>End</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">trEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LEFT</span><span class="p">;</span></span>
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167
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="p">}</span></span>
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168
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> </span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">tr<span class="idiff left right">im</span>End</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">trEnd</span><span class="p">){</span></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rCutPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC176" 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">@@ -211,6 +215,11 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC216" 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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213
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> </span>
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218
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<pre style="margin: 0;">+<span id="LC218" 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="p">){</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" 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_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;">qIndex</span><span class="p">).</span><span class="n" style="color: #333;">rcAdapter</span><span class="p">)</span> <span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">rmAdapter</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="LC220" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">rmAdapterRC</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="LC221" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"> </span>
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214
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// count number of removals for each query</span></span>
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215
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <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;">qIndex</span><span class="p">).</span><span class="n" style="color: #333;">rmOverlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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216
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225
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<pre style="margin: 0;"> <span id="LC225" 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">@@ -233,9 +242,9 @@ public:</td>
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> </span>
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234
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// valid alignment, not neccesarily removal</span></span>
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235
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> </span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_<span class="idiff left">randTag</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">am</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">rand</span>Tag</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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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_<span class="idiff left">umiTags</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">am</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">umi</span>Tag</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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237
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">);</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">rand</span>Tag</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqRead</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">am</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">umi</span>Tag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="p">}</span></span>
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240
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// alignment stats</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,9 +253,9 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">performRemoval</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Sequence removal:"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tr<span class="idiff left">imEnd</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">LEFT</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">trim</span>End</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;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" left side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" 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;">tr<span class="idiff left">imEnd</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</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">trim</span>End</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">)</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" right side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" any side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tr<span class="idiff left">End</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">LEFT</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">tr</span>End</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;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" left side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC257" 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;">tr<span class="idiff left">End</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</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">tr</span>End</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RTAIL</span><span class="p">)</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" right side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" any side</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Sequence detection, no removal:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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252
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> </span>
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<li id="e2dac719d776653f92cfaedf47045ae0c6d30b38">
<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#e2dac719d776653f92cfaedf47045ae0c6d30b38"><strong>src/SeqAlignAlgo.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">@@ -21,16 +21,14 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// TScoreSimple m_score;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">TScoreMatrix</span> <span class="n" style="color: #333;">m_scoreMatrix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_<span class="idiff left right">randTag</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_<span class="idiff left right">umiTags</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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;">LogAlign</span> <span class="n" style="color: #333;">m_log</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="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;">m_trimEnd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">SeqAlignAlgo</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapCost</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 class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">m_randTag</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">randTag</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC32" 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>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">m_trimEnd</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="LC29" class="line" lang="c"> <span class="n" style="color: #333;">SeqAlignAlgo</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Options</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gapCost</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" 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="LC31" 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>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC33" 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;">seqan</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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">@@ -50,7 +48,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="p">};</span></span>
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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>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignGlobal</span><span class="p">(</span><span class="n" style="color: #333;">TAlignResults</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;">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="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;">idxAl</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">alignGlobal</span><span class="p">(</span><span class="n" style="color: #333;">TAlignResults</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;">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="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;">idxAl</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">flexbar</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">TrimEnd</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trimEnd</span></span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC53" 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="LC54" 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;">seqan</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">@@ -69,12 +67,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">cycle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RESULTS</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">m_trimEnd</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</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">m_</span>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="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">trimEnd</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</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;">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="LC71" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">AlignConfig</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ac</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">ascores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">globalAlignment</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;">m_scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">ac</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC77" 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">m_trimEnd</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">LEFT</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">m_</span>trimEnd</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="LC75" 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">trimEnd</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">LEFT</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;">trimEnd</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="LC76" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">AlignConfig</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ac</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;">alignments</span><span class="p">.</span><span class="n" style="color: #333;">ascores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">globalAlignment</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;">m_scoreMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">ac</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,7 +111,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">alString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_<span class="idiff left">randTag</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">rand</span>Tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_<span class="idiff left">umiTags</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">umi</span>Tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> </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;">TRowIterator</span> <span class="n" style="color: #333;">it1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</span><span class="p">(</span><span class="n" style="color: #333;">row1</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">@@ -130,7 +128,7 @@ public:</td>
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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;">isGap</span><span class="p">(</span><span class="n" style="color: #333;">it1</span><span class="p">))</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;">gapsR</span><span class="p">;</span></span>
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131
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129
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<pre style="margin: 0;"> <span id="LC129" 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;">isGap</span><span class="p">(</span><span class="n" style="color: #333;">it2</span><span class="p">))</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;">gapsA</span><span class="p">;</span></span>
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132
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130
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<pre style="margin: 0;"> <span id="LC130" 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;">it1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">)</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;">mismatches</span><span class="p">;</span></span>
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133
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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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_<span class="idiff left">randTag</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="n" style="color: #333;"><span class="idiff">it2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'N'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">rand</span>Tag</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">TChar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC131" 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_<span class="idiff left">umiTags</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="n" style="color: #333;"><span class="idiff">it2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'N'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">umi</span>Tag</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">TChar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">alPos</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it2</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/flexbar/compare/2492335f3e5e7a220cd53101d01847f863aa3a43...6e3443441c2f480a838b07e7c722c2507db86230#aa49d3edaf982a9eb8ecad9841b1507eba6ed69a"><strong>src/SeqInput.h</strong></a>
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<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">@@ -117,6 +117,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">m_preTrimEnd</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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121
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_preTrimEnd</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,6 +128,7 @@ public:</td>
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128
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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_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">)</span></span>
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128
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">quals</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;">prefix</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">quals</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;">idx</span><span class="p">);</span></span>
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129
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="p">}</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> </span>
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130
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132
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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_qtrim</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">QOFF</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">m_qtrimPostRm</span><span class="p">){</span></span>
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131
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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;">qualTrim</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">i</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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132
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="p">}</span></span>
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