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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastp/-/commit/2c6af5bd4adfd804d6d478e3efcd59b07e5720e6">2c6af5bd</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2021-11-19T16:29:47+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.23.1+dfsg</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#742351309009b70e28c04c50b75d5287975926bb">
src/common.h
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<a href="#8f848fe3bda53a34670cfd820d42d2e80c6a1baf">
src/peprocessor.cpp
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/fastp/-/commit/2c6af5bd4adfd804d6d478e3efcd59b07e5720e6#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,7 +64,8 @@ A tool designed to provide fast all-in-one preprocessing for FastQ files. This t</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p">11.</span> support long reads (data from PacBio / Nanopore devices).</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">12.</span> support reading from STDIN and writing to STDOUT</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="p">13.</span> support interleaved input</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown"><span class="p">14.</span> ...</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p">14.</span> support ultra-fast FASTQ-level deduplication</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="p">15.</span> ...</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown">This tool is being intensively developed, and new features can be implemented soon if they are considered useful. If you have any additional requirement for <span class="sb" style="color: #d14;">`fastp`</span>, please file an issue:https://github.com/OpenGene/fastp/issues/new</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,15 +94,15 @@ https://anaconda.org/bioconda/fastp/badges/version.svg)](https://anaconda.org/bi</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">conda <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-c</span> bioconda fastp</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## or download the latest prebuilt binary for Linux users</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown">T<span class="idiff left right">t</span>his binary was compiled on CentOS, and tested on CentOS/Ubuntu</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">This binary was compiled on CentOS, and tested on CentOS/Ubuntu</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="p">```</span><span class="nl">shell</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># download the latest build</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown">wget http://opengene.org/fastp/fastp</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">chmod </span>a+x ./fastp</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># or download specified version, i.e. fastp v0.2<span class="idiff left right">0</span>.1</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown">wget http://opengene.org/fastp/fastp.0.2<span class="idiff left right">0</span>.1</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mv </span>fastp.0.2<span class="idiff left right">0</span>.1 fastp</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># or download specified version, i.e. fastp v0.2<span class="idiff left right">3</span>.1</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">wget http://opengene.org/fastp/fastp.0.2<span class="idiff left right">3</span>.1</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mv </span>fastp.0.2<span class="idiff left right">3</span>.1 fastp</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">chmod </span>a+x ./fastp</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## or compile from source</span></span>
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<a href="https://salsa.debian.org/med-team/fastp/-/commit/2c6af5bd4adfd804d6d478e3efcd59b07e5720e6#742351309009b70e28c04c50b75d5287975926bb"><strong>src/common.h</strong></a>
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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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<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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<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 "0.23.<span class="idiff left right">0</span>"</span></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 "0.23.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/fastp/-/commit/2c6af5bd4adfd804d6d478e3efcd59b07e5720e6#8f848fe3bda53a34670cfd820d42d2e80c6a1baf"><strong>src/peprocessor.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">@@ -109,11 +109,11 @@ void PairEndProcessor::closeOutput() {</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mUnpairedLeftWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">mUnpairedLeftWriter</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">mLeftWriter</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="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">m<span class="idiff left right">Unpaired</span>LeftWriter</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="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mUnpairedRightWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">mUnpairedRightWriter</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">mRightWriter</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="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">m<span class="idiff left right">Unpaired</span>RightWriter</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="LC117" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></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">@@ -555,11 +555,15 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T</td>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"> <span class="p">}</span> <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;">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;">result2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PASS_FILTER</span><span class="p">)</span> <span class="p">{</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mUnpairedLeftWriter</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;">mUnpairedRightWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mUnpairedRightWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp"> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendToString</span><span class="p">(</span><span class="n" style="color: #333;">unpairedOut2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mFailedWriter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">or1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendToStringWithTag</span><span class="p">(</span><span class="n" style="color: #333;">failedOut</span><span class="p">,</span><span class="n" style="color: #333;">FAILED_TYPES</span><span class="p">[</span><span class="n" style="color: #333;">result1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="p">}</span> <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;">mUnpairedLeftWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">appendToString</span><span class="p">(</span><span class="n" style="color: #333;">unpairedOut1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mFailedWriter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC565" 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;">appendToStringWithTag</span><span class="p">(</span><span class="n" style="color: #333;">failedOut</span><span class="p">,</span><span class="n" style="color: #333;">FAILED_TYPES</span><span class="p">[</span><span class="n" style="color: #333;">result1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mFailedWriter</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC568" 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;">appendToStringWithTag</span><span class="p">(</span><span class="n" style="color: #333;">failedOut</span><span class="p">,</span> <span class="n" style="color: #333;">FAILED_TYPES</span><span class="p">[</span><span class="n" style="color: #333;">result1</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC569" 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;">appendToStringWithTag</span><span class="p">(</span><span class="n" style="color: #333;">failedOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"paired_read_is_failing"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="648" style="width: 35px; color: rgba(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">@@ -648,9 +652,6 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T</td>
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648
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> <span class="p">}</span> <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;">mUnpairedLeftWriter</span><span class="p">)</span> <span class="p">{</span></span>
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">mUnpairedLeftWriter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">unpairedOut1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"> <span class="n" style="color: #333;">unpairedOut1</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="LC651" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">mUnpairedLeftWriter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">input</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">unpairedOut2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">unpairedOut2</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="LC655" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC657" 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;">split</span><span class="p">.</span><span class="n" style="color: #333;">byFileLines</span><span class="p">)</span></span>
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