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<h3>

Dylan Aïssi pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755">fcc688de</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2020-04-11T22:14:24+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.20.1+dfsg</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#742351309009b70e28c04c50b75d5287975926bb">

src/common.h

</a>

</li>

<li class="file-stats">

<a href="#ee6c332e289766c695163be4a50376249ec9660a">

src/htmlreporter.cpp

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<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">

src/main.cpp

</a>

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<li class="file-stats">

<a href="#8ecb4c063e8d1443c6f8b162726b449768199c57">

src/options.cpp

</a>

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<li class="file-stats">

<a href="#111d7d08de2d396195029a9e93eebc9942053b09">

src/options.h

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<a href="#8f848fe3bda53a34670cfd820d42d2e80c6a1baf">

src/peprocessor.cpp

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<a href="#57c3c58e9b5fb7fc752c23a0041722bf1cf56a8c">

src/read.cpp

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<li class="file-stats">

<a href="#cbc2544e131fa11c629c823f2f35705b18f2e1c0">

src/read.h

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<a href="#5b8a2cc46c907b1e3eac9d3246b881d83541391a">

src/seprocessor.cpp

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<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -304,7 +304,7 @@ options:</td>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="markdown">  <span class="nt" style="color: #000080;">-I</span>, <span class="nt" style="color: #000080;">--in2</span>                          read2 input file name <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="markdown">  <span class="nt" style="color: #000080;">-O</span>, <span class="nt" style="color: #000080;">--out2</span>                           read2 output file name <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--unpaired1</span>                      <span class="k" style="font-weight: 600;">for </span>PE input, <span class="k" style="font-weight: 600;">if </span>read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--unpaired2</span>                      <span class="k" style="font-weight: 600;">for </span>PE input, <span class="k" style="font-weight: 600;">if </span>read2 passed QC but read1 not, it will be written to unpaired2. If <span class="nt" style="color: #000080;">--unpaired2</span> is same as <span class="nt" style="color: #000080;">--u<span class="idiff left right">m</span>paired1</span> <span class="o" style="font-weight: 600;">(</span>default mode<span class="o" style="font-weight: 600;">)</span>, both unpaired reads will be written to this same file. <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--unpaired2</span>                      <span class="k" style="font-weight: 600;">for </span>PE input, <span class="k" style="font-weight: 600;">if </span>read2 passed QC but read1 not, it will be written to unpaired2. If <span class="nt" style="color: #000080;">--unpaired2</span> is same as <span class="nt" style="color: #000080;">--u<span class="idiff left right">n</span>paired1</span> <span class="o" style="font-weight: 600;">(</span>default mode<span class="o" style="font-weight: 600;">)</span>, both unpaired reads will be written to this same file. <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--failed_out</span>                     specify the file to store reads that cannot pass the filters. <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown">  <span class="nt" style="color: #000080;">-m</span>, <span class="nt" style="color: #000080;">--merge</span>                          <span class="k" style="font-weight: 600;">for </span>paired-end input, merge each pair of reads into a single <span class="nb" style="color: #0086b3;">read </span><span class="k" style="font-weight: 600;">if </span>they are overlapped. The merged reads will be written to the file given by <span class="nt" style="color: #000080;">--merged_out</span>, the unmerged reads will be written to the files specified by <span class="nt" style="color: #000080;">--out1</span> and <span class="nt" style="color: #000080;">--out2</span><span class="nb" style="color: #0086b3;">.</span> The merging mode is disabled by default.</span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--merged_out</span>                     <span class="k" style="font-weight: 600;">in </span>the merging mode, specify the file name to store merged output, or specify <span class="nt" style="color: #000080;">--stdout</span> to stream the merged output <span class="o" style="font-weight: 600;">(</span>string <span class="o" style="font-weight: 600;">[=])</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="markdown"><span class="s1" style="color: #d14;">      --interleaved_in                 indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="markdown"><span class="s1" style="color: #d14;">      --reads_to_process             specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"><span class="s1" style="color: #d14;">      --dont_overwrite               don'</span>t overwrite existing files. Overwritting is allowed by default.</span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown">      <span class="nt" style="color: #000080;">--fix_mgi_id</span>                     the MGI FASTQ ID format is not compatible with many BAM operation tools, <span class="nb" style="color: #0086b3;">enable </span>this option to fix it.</span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown">  </span>

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320

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="markdown">  <span class="c" style="color: #998; font-style: italic;"># adapter trimming options</span></span>

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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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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown">  <span class="nt" style="color: #000080;">-A</span>, <span class="nt" style="color: #000080;">--disable_adapter_trimming</span>     adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled</span>

</pre>

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<br>

</li>

<li id="742351309009b70e28c04c50b75d5287975926bb">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#742351309009b70e28c04c50b75d5287975926bb"><strong>src/common.h</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef COMMON_H</span></span>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define COMMON_H</span></span>

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3

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FASTP_VER "0.20.<span class="idiff left right">0</span>"</span></span>

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FASTP_VER "0.20.<span class="idiff left right">1</span>"</span></span>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _DEBUG false</span></span>

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7

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

7

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

</pre>

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<li id="ee6c332e289766c695163be4a50376249ec9660a">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#ee6c332e289766c695163be4a50376249ec9660a"><strong>src/htmlreporter.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); 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="406" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -406,7 +406,7 @@ void HtmlReporter::printCSS(ofstream& ofs){</td>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC407" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HtmlReporter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printJS</span><span class="p">(</span><span class="n" style="color: #333;">ofstream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ofs</span><span class="p">){</span></span>

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<td class="diff-line-num old old_line" data-linenumber="409" style="width: 35px; color: rgba(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="409" style="width: 35px; color: rgba(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="LC409" class="line" lang="cpp">    <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<script src='http<span class="idiff left right">s://cdn.plot.ly/plotly-latest</span>.min.js'></script>"</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="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp">    <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<script src='http<span class="idiff left right">://opengene.org/plotly-1.2.0</span>.min.js'></script>"</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="410" style="width: 35px; color: rgba(0,0,0,0.3); 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="410" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC410" class="line" lang="cpp">    <span class="n" style="color: #333;">ofs</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;"><script type=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">text/javascript</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); 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="411" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC411" class="line" lang="cpp">    <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    function showOrHide(divname) {"</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="LC412" class="line" lang="cpp">    <span class="n" style="color: #333;">ofs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"        div = document.getElementById(divname);"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="b958235ee8db37bcaceda04b6d55553b450c2db4">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +36,7 @@ int main(int argc, char* argv[]){</td>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"in2"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">,</span> <span class="s" style="color: #d14;">"read2 input file name"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"out2"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'O'</span><span class="p">,</span> <span class="s" style="color: #d14;">"read2 output file name"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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

38

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

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"unpaired1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"unpaired2"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --u<span class="idiff left right">m</span>paired1 (default mode), both unpaired reads will be written to this same file."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"unpaired2"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --u<span class="idiff left right">n</span>paired1 (default mode), both unpaired reads will be written to this same file."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

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

40

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

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"failed_out"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"specify the file to store reads that cannot pass the filters."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"merge"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">,</span> <span class="s" style="color: #d14;">"for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default."</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"merged_out"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,6 +48,7 @@ int main(int argc, char* argv[]){</td>

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

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"interleaved_in"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default."</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"reads_to_process"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"specify how many reads/pairs to be processed. Default 0 means process all reads."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"dont_overwrite"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"don't overwrite existing files. Overwritting is allowed by default."</span><span class="p">);</span></span>

</pre>

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

</td>

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

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"fix_mgi_id"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'V'</span><span class="p">,</span> <span class="s" style="color: #d14;">"output verbose log information (i.e. when every 1M reads are processed)."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// adapter</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); 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="178" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -177,6 +178,7 @@ int main(int argc, char* argv[]){</td>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); 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="178" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC178" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">outputToSTDOUT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">exist</span><span class="p">(</span><span class="s" style="color: #d14;">"stdout"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); 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="179" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">interleavedInput</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">exist</span><span class="p">(</span><span class="s" style="color: #d14;">"interleaved_in"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); 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="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">exist</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fixMGI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">exist</span><span class="p">(</span><span class="s" style="color: #d14;">"fix_mgi_id"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); 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="183" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC183" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// merge PE</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">.</span><span class="n" style="color: #333;">enabled</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">exist</span><span class="p">(</span><span class="s" style="color: #d14;">"merge"</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="8ecb4c063e8d1443c6f8b162726b449768199c57">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#8ecb4c063e8d1443c6f8b162726b449768199c57"><strong>src/options.cpp</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +26,7 @@ Options::Options(){</td>

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

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp">    <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">    <span class="n" style="color: #333;">seqLen1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">151</span><span class="p">;</span></span>

</pre>

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

28

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp">    <span class="n" style="color: #333;">seqLen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">151</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">    <span class="n" style="color: #333;">fixMGI</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="LC30" class="line" lang="cpp"><span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">()</span> <span class="p">{</span></span>

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<li id="111d7d08de2d396195029a9e93eebc9942053b09">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#111d7d08de2d396195029a9e93eebc9942053b09"><strong>src/options.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -325,6 +325,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">interleavedInput</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// only process first N reads</span></span>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC327" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">readsToProcess</span><span class="p">;</span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// fix the MGI ID tailing issue</span></span>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fixMGI</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// worker thread number</span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// trimming options</span></span>

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<li id="8f848fe3bda53a34670cfd820d42d2e80c6a1baf">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#8f848fe3bda53a34670cfd820d42d2e80c6a1baf"><strong>src/peprocessor.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -338,6 +338,11 @@ bool PairEndProcessor::processPairEnd(ReadPairPack* pack, ThreadConfig* config){</td>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="diff-line-num old_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">

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

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<td class="diff-line-num new old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); 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="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// fix MGI</span></span>

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<td class="diff-line-num new old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); 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="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixMGI</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); 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="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp">            <span class="n" style="color: #333;">or1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixMGI</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp">            <span class="n" style="color: #333;">or2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixMGI</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// umi processing</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">enabled</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp">            <span class="n" style="color: #333;">mUmiProcessor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">process</span><span class="p">(</span><span class="n" style="color: #333;">or1</span><span class="p">,</span> <span class="n" style="color: #333;">or2</span><span class="p">);</span></span>

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<br>

</li>

<li id="57c3c58e9b5fb7fc752c23a0041722bf1cf56a8c">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#57c3c58e9b5fb7fc752c23a0041722bf1cf56a8c"><strong>src/read.cpp</strong></a>

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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">@@ -135,6 +135,17 @@ string Read::toStringWithTag(string tag) {</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mName</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;">tag</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;">mSeq</span><span class="p">.</span><span class="n" style="color: #333;">mStr</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;">mStrand</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;">mQuality</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="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixMGI</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mName</span><span class="p">.</span><span class="n" style="color: #333;">length</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">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mName</span><span class="p">[</span><span class="n" style="color: #333;">len</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="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mName</span><span class="p">[</span><span class="n" style="color: #333;">len</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="sc" style="color: #d14;">'2'</span><span class="p">)</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">

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mName</span><span class="p">[</span><span class="n" style="color: #333;">len</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="sc" style="color: #d14;">'/'</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">                  <span class="n" style="color: #333;">mName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mName</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">len</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mName</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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="LC143" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">test</span><span class="p">(){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  <span class="n" style="color: #333;">Read</span> <span class="n" style="color: #333;">r</span><span class="p">(</span><span class="s" style="color: #d14;">"@NS500713:64:HFKJJBGXY:1:11101:20469:1097 1:N:0:TATAGCCT+GGTCCCGA"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">          <span class="s" style="color: #d14;">"CTCTTGGACTCTAACACTGTTTTTTCTTATGAAAACACAGGAGTGATGACTAGTTGAGTGCATTCTTATGAGACTCATAGTCATTCTATGATGTAGTTTTCCTTAGGAGGACATTTTTTACATGAAATTATTAACCTAAATAGAGTTGATC"</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="cbc2544e131fa11c629c823f2f35705b18f2e1c0">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#cbc2544e131fa11c629c823f2f35705b18f2e1c0"><strong>src/read.h</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,6 +31,7 @@ public:</td>

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31

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31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>

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

32

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32

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">convertPhred64To33</span><span class="p">();</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">trimFront</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fixMGI</span><span class="p">();</span></span>

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="nl">public:</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">test</span><span class="p">();</span></span>

</pre>

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<br>

</li>

<li id="5b8a2cc46c907b1e3eac9d3246b881d83541391a">

<a href="https://salsa.debian.org/med-team/fastp/-/commit/fcc688de8b9e557ac57e748c83f2c7b16c6a6755#5b8a2cc46c907b1e3eac9d3246b881d83541391a"><strong>src/seprocessor.cpp</strong></a>

<hr>

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

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

<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 +211,11 @@ bool SingleEndProcessor::processSingleEnd(ReadPack* pack, ThreadConfig* config){</td>

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

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">or1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC212" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// fix MGI</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixMGI</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp">            <span class="n" style="color: #333;">or1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixMGI</span><span class="p">();</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// umi processing</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">enabled</span><span class="p">)</span></span>

</pre>

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