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GitLab

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<h3>

Steffen Möller pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5">63ea0026</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-08-21T21:46:35+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.7.5c+dfsg</pre>

</li>

</ul>

<h4>24 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#1d6ebb42152a3125296c8f3df8bc34651da72448">

doc/STARmanual.pdf

</a>

</li>

<li class="file-stats">

<a href="#5a5668ccb427693fe0e7ea2e054229206cb91b0a">

extras/doc-latex/STARmanual.tex

</a>

</li>

<li class="file-stats">

<a href="#dd357fd519066773532862e75ebb9276945c8fe5">

extras/doc-latex/parametersDefault.tex

</a>

</li>

<li class="file-stats">

<a href="#8955c7301dc01c7f9b2a350f2aee6066e91f8f83">

extras/docker/Dockerfile

</a>

</li>

<li class="file-stats">

<a href="#165858b6de35f6f7c794dcfe8e28a97119310ec8">

source/ErrorWarning.cpp

</a>

</li>

<li class="file-stats">

<a href="#91be571d30070624a6131ee976f3c342107c4696">

source/GTF.cpp

</a>

</li>

<li class="file-stats">

<a href="#f4eb1c9c89d8a6664c03d29afd21f3104689a8d9">

source/Genome_genomeGenerate.cpp

</a>

</li>

<li class="file-stats">

<a href="#a0b6c92785c5892df94b89d21ead0dc460541d74">

source/IncludeDefine.h

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<li class="file-stats">

<a href="#6ae9e88712056a2abd55911f4d3a7d8b8145819c">

source/Makefile

</a>

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<li class="file-stats">

<a href="#6e7e9199db44be8b0f606c7c21db10763fc8b0eb">

source/Parameters.cpp

</a>

</li>

<li class="file-stats">

<a href="#bf27f52254916f0127a15b2aa4242b8679bb9815">

source/ParametersSolo.cpp

</a>

</li>

<li class="file-stats">

<a href="#b6bbf0242e5e8b3ccfc1f5b5a8ccf033fb5ae809">

source/Parameters_openReadsFiles.cpp

</a>

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<li class="file-stats">

<a href="#b7114790c4e1e6b022e2111cc5b7c713050c42a0">

source/Parameters_readSAMheader.cpp

</a>

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<li class="file-stats">

<a href="#7245d12cb1ad9b44f08daa0ab3e702d4bed39531">

source/ReadAlignChunk_processChunks.cpp

</a>

</li>

<li class="file-stats">

<a href="#764c3cfc36fad2f293fd356112b8836ea61e0b02">

source/ReadAlign_alignBAM.cpp

</a>

</li>

<li class="file-stats">

<a href="#4896a67af34962395106d0bd2c41b227ffde5a58">

source/STAR.cpp

</a>

</li>

<li class="file-stats">

<a href="#8ab4cbdfbf463cf0757c6b325b3b1b4d95720372">

source/SoloFeature_collapseUMI.cpp

</a>

</li>

<li class="file-stats">

<a href="#e79ceffd8a1458e9765b7ce8380e4e8568543d53">

source/Transcriptome_classifyAlign.cpp

</a>

</li>

<li class="file-stats">

<a href="#46ef577d4524cc6123d3e3cfa053a5ca85c35274">

source/VERSION

</a>

</li>

<li class="file-stats">

<a href="#d1de46dc38c5a41c3a5dc9d20994daf72784ac7d">

source/genomeScanFastaFiles.cpp

</a>

</li>

<li class="file-stats">

<a href="#14e4f2926f46a184cc81f069a1550cb71e369b6d">

source/parametersDefault

</a>

</li>

<li class="file-stats">

<a href="#8d3b9ff64d8dd5569149f7e7f75554bcab49ad30">

source/readLoad.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.7.5c --- 2020/08/16</span></span>

</pre>

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

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

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==========================</span></span>

</pre>

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

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

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;">Bug-fix release.</span></span>

</pre>

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

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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="markdown"><span class="gh" style="color: #999;">----------------</span></span>

</pre>

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

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5

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

</pre>

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

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

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">*</span> Issue #988: proceed reading from GTF after a warning that exon end is past chromosome end.</span>

</pre>

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

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Issue #978: fixed corrupted transcriptInfo.tab in genome generation for cases where GTF file contains extra chromosomes not present in FASTA files.</span>

</pre>

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

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">*</span> Issue #945: otuput GX/GN for --soloFeatures GeneFull .</span>

</pre>

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

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> Implemented removal of control characters from the ends of input read lines, for compatibility with files pre-processed on Windows.</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.7.5b --- 2020/08/01</span></span>

</pre>

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12

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==========================</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gh" style="color: #999;">Bug-fix release.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------</span></span>

</pre>

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15

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> Issue #558: Fixed a bug that can cause a seg-fault in STARsolo run with paired-end reads that have protruding ends.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> Issue #952: Increased the maximum allowed length of the SAM tags in the input SAM files.</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">*</span> Issue #955: fixed seg-fault-causing bug for --soloFeatures SJ option.</span>

</pre>

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

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

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> Issue #963: When reading GTF file, skip any exons that extend past the end of the chromosome, and give a warning.</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> Issue #965: output genome sizes with and without padding into Log.out.</span>

</pre>

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

1

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

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">*</span> Docker build: switched to debian:stable-slim in the Dockerfile.</span>

</pre>

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2

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">*</span> --soloType CB_samTagOut now allows output of (uncorrected) UMI sequences and quality scores with SAM tags UR and UY.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">*</span> Throw an error if FIFO file cannot be created on non-Linux partitions.</span>

</pre>

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3

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

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.7.5a 2020/06/16</span></span>

</pre>

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

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.7</span></span>

</pre>

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

2

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

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">Spliced Transcripts Alignment to a Reference</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC4" class="line" lang="markdown">© Alexander Dobin, 2009-20<span class="idiff left right">19</span></span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">© Alexander Dobin, 2009-20<span class="idiff left right">20</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">https://www.ncbi.nlm.nih.gov/pubmed/23104886</span>

</pre>

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

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

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">AUTHOR/SUPPORT</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,9 +35,9 @@ Download the latest [release from](https://github.com/alexdobin/STAR/releases) a</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</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="markdown"><span class="c" style="color: #998; font-style: italic;"># Get latest STAR source from releases</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" 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="38" 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="LC38" class="line" lang="markdown">wget https://github.com/alexdobin/STAR/archive/2.7.5<span class="idiff left right">a</span>.tar.gz</span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="38" 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="markdown"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> 2.7.5<span class="idiff left right">a</span>.tar.gz</span>

</pre>

</td>

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

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<td class="diff-line-num new_line old" data-linenumber="38" 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="LC40" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>STAR-2.7.5<span class="idiff left right">a</span></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">wget https://github.com/alexdobin/STAR/archive/2.7.5<span class="idiff left right">c</span>.tar.gz</span>

</pre>

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

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<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="markdown"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzf</span> 2.7.5<span class="idiff left right">c</span>.tar.gz</span>

</pre>

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

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

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>STAR-2.7.5<span class="idiff left right">c</span></span>

</pre>

</td>

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Alternatively, get STAR source using git</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">git clone https://github.com/alexdobin/STAR.git</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="1d6ebb42152a3125296c8f3df8bc34651da72448">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#1d6ebb42152a3125296c8f3df8bc34651da72448"><strong>doc/STARmanual.pdf</strong></a>

<hr>

No preview for this file type

<br>

</li>

<li id="5a5668ccb427693fe0e7ea2e054229206cb91b0a">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#5a5668ccb427693fe0e7ea2e054229206cb91b0a"><strong>extras/doc-latex/STARmanual.tex</strong></a>

<hr>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="tex"><span class="k" style="font-weight: 600;">\newcommand</span><span class="p">{</span><span class="k" style="font-weight: 600;">\sechyperref</span><span class="p">}</span>[1]<span class="p">{</span><span class="k" style="font-weight: 600;">\hyperref</span><span class="na" style="color: #008080;">[#1]</span><span class="p">{</span>Section <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>#1<span class="p">}</span>. <span class="k" style="font-weight: 600;">\nameref</span><span class="p">{</span>#1<span class="p">}}}</span></span>

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="tex"><span class="k" style="font-weight: 600;">\title</span><span class="p">{</span>STAR manual 2.7.5<span class="idiff left right">a</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="tex"><span class="k" style="font-weight: 600;">\title</span><span class="p">{</span>STAR manual 2.7.5<span class="idiff left right">c</span><span class="p">}</span></span>

</pre>

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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="tex"><span class="k" style="font-weight: 600;">\author</span><span class="p">{</span>Alexander Dobin<span class="k" style="font-weight: 600;">\\</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="tex">dobin@cshl.edu<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="tex"><span class="k" style="font-weight: 600;">\maketitle</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -292,28 +292,83 @@ The \opt{outSAMmultNmax} parameter limits the number of output alignments (SAM l</td>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsubsection</span><span class="p">{</span>SAM attributes.<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="tex">The SAM attributes can be specified by the user using <span class="k" style="font-weight: 600;">\opt</span><span class="p">{</span>outSAMattributes<span class="p">}</span> <span class="k" style="font-weight: 600;">\optvr</span><span class="p">{</span>A1 A2 A3 ...<span class="p">}</span> option which accept a list of 2-character SAM attributes. The implemented attributes are: <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NH HI NM MD AS nM jM jI XS<span class="p">}</span>. By default, STAR outputs <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NH HI AS nM<span class="p">}</span> attributes.</span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{itemize}</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="tex">The SAM attributes can be specified by the user using <span class="k" style="font-weight: 600;">\opt</span><span class="p">{</span>outSAMattributes<span class="p">}</span> <span class="k" style="font-weight: 600;">\optvr</span><span class="p">{</span>A1 A2 A3 ...<span class="p">}</span> option which accept a list of 2-character SAM attributes. The attributes can be listed in any order, and will be recorded in that order in the SAM file. By default, STAR outputs <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NH HI AS nM<span class="p">}</span> attributes.</span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="tex"></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{itemize}</span>[itemsep=1pt]</span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span>  </span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>Presets:<span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>None<span class="p">}</span> : No SAM attributes</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NH HI NM MD<span class="p">}</span> : have standard meaning as defined in the SAM format specifications.</span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>Standard<span class="p">}</span> : NH HI AS nM</span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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

308

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>All<span class="p">}</span> : NH HI AS nM NM MD jM jI MC ch     </span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>Alignment:<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

311

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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312

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="313" 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="LC300" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>AS<span class="p">}</span> : id the local alignment score (paired for paired-end reads). </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NH<span class="p">}</span> : number of loci the reads maps to: <span class="p">$</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">$</span> for unique mappers, <span class="p">$</span><span class="nb" style="color: #0086b3;">></span><span class="m" style="color: #099;">1</span><span class="p">$</span> for multimappers. Standard SAM tag.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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315

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="316" 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="LC302" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>nM<span class="p">}</span> : is the number of mismatches per (paired) alignment, not to be confused with <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NM<span class="p">}</span>, which is the number of mismatches in each mate.</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>HI<span class="p">}</span>  : multiple alignment index, starts with --outSAMattrIHstart (<span class="p">$</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">$</span> by default). Standard SAM tag.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>AS<span class="p">}</span> : local alignment score, <span class="p">$</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/-</span><span class="m" style="color: #099;">1</span><span class="p">$</span> for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NM<span class="p">}</span> : edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>nM<span class="p">}</span> : number of mismatches per (paired) alignment, not to be confused with <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>NM<span class="p">}</span>, which is the number of mismatches+indels in each mate.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC328" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>jM:B:c,M1,M2,...<span class="p">}</span> : intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>MD<span class="p">}</span> : string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>jI:B:I,Start1,End1,Start2,End2,...<span class="p">}</span> : Start and End of introns for all junctions (1-based).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>jM jI<span class="p">}</span> : attributes require samtools 0.1.18 or later, and were reported to be incompatible with some downstream tools such as Cufflinks.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>Variation:<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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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="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vA<span class="p">}</span> : variant allele.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vG<span class="p">}</span> : genomic coordinate of the variant overlapped by the read.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vW<span class="p">}</span> : WASP filtering tag, see detailed description in Section <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>section:WASP<span class="p">}</span>. Requires <span class="k" style="font-weight: 600;">\opt</span><span class="p">{</span>waspOutputMode<span class="p">}</span> <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>SAMtag<span class="p">}</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="tex"></span>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>STARsolo:<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vA<span class="p">}</span> : variant allele</span>

</pre>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>CR CY UR UY<span class="p">}</span> : sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing, not error corrected.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vG<span class="p">}</span> : genomic coordiante of the variant overlapped by the read</span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>GX GN<span class="p">}</span> : gene ID and name.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>vW<span class="p">}</span> : WASP filtering tag, see detailed description in Section <span class="k" style="font-weight: 600;">\ref</span><span class="p">{</span>section:WASP<span class="p">}</span>==. Requires --waspOutputMode SAMtag</span>

</pre>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>CB UB<span class="p">}</span> : error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires <span class="k" style="font-weight: 600;">\opt</span><span class="p">{</span>outSAMtype<span class="p">}</span> <span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>BAM SortedByCoordinate<span class="p">}</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>CR CY UR UY<span class="p">}</span> : STARsolo: sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing, not error corrected</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); 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="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

362

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

<pre style="margin: 0;">+<span id="LC362" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>sM<span class="p">}</span> : assessment of CB and UMI.</span>

</pre>

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363

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); 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="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); 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="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>sS<span class="p">}</span> : sequence of the entire barcode (CB,UMI,adapter...).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); 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="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>sQ<span class="p">}</span> : quality of the entire barcode.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="tex"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="tex"><span class="k" style="font-weight: 600;">\textbf</span><span class="p">{</span>Unmapped reads:<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="tex"><span class="k" style="font-weight: 600;">\item</span><span class="na" style="color: #008080;">[]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optv</span><span class="p">{</span>uT<span class="p">}</span> : for unmapped reads, reason for not mapping:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="tex">           <span class="nt" style="color: #000080;">\begin{itemize}</span>[noitemsep,topsep=-3pt]</span>

</pre>

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</li>

<li id="dd357fd519066773532862e75ebb9276945c8fe5">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#dd357fd519066773532862e75ebb9276945c8fe5"><strong>extras/doc-latex/parametersDefault.tex</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">@@ -291,35 +291,47 @@</td>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optName</span><span class="p">{</span>outSAMattributes<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC293" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optValue</span><span class="p">{</span>Standard<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>string: a string of desired SAM attributes, in the order desired for the output SAM<span class="p">}</span> </span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>string: a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.<span class="p">}</span> </span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>***Presets:<span class="p">}</span> </span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>NH HI AS nM NM MD jM jI XS MC ch<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>any combination in any order<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>None<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>no attributes<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>Standard<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>NH HI AS nM<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>All<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>NH HI AS nM NM MD jM jI MC ch<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>variation:<span class="p">}</span> </span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>***Alignment:<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>NH<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>number of loci the reads maps to: =1 for unique mappers, <span class="p">{</span><span class="k" style="font-weight: 600;">\textgreater</span><span class="p">}</span>1 for multimappers. Standard SAM tag.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>HI<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>multiple alignment index, starts with --outSAMattrIHstart (=1 by default). Standard SAM tag.<span class="p">}</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>AS<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>local alignment score, +1/-1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>nM<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>number of mismatches. For PE reads, sum over two mates.<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>NM<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>MD<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>jM<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>jI<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>start and end of introns for all junctions (1-based).<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>XS<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>alignment strand according to --outSAMstrandField.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>MC<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>mate's CIGAR string. Standard SAM tag.<span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>ch<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>marks all segment of all chimeric alingments for --chimOutType WithinBAM output.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>***Variation:<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vA<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>variant allele<span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>ha<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vG<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>genomic coordinate of the variant overlapped by the read<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vG<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>genomic coordinate of the variant overlapped by the read.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vW<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --waspOutputMode SAMtag.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>STARsolo:<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span><span class="idiff left right">***</span>STARsolo:<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>CR CY UR UY<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>CR CY UR UY<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>GX GN<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>gene ID and gene name.<span class="p">}</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>CB UB<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate.<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>sM<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>assessment of CB and UMI<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="313" 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="LC313" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="314" 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="LC314" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>sS          ... sequence of the entire barcode (CB,UMI,adapter...)<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>sQ<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>quality of the entire barcode<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="317" 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="LC317" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>GX GN<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>gene ID and gene name<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>sM<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>assessment of CB and UMI.<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>sS<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>sequence of the entire barcode (CB,UMI,adapter).<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>sQ<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>quality of the entire barcode.<span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC329" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="330" 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="LC319" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span>Unsupported/undocumented:<span class="p">}</span> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optLine</span><span class="p">{</span><span class="idiff left right">***</span>Unsupported/undocumented:<span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="tex"><span class="nt" style="color: #000080;">\begin{optOptTable}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>rB<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>alignment block read/genomic coordinates<span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="322" 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="LC322" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vR<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>read coordinate of the variant<span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>ha<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid .<span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>rB<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>alignment block read/genomic coordinates.<span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optOpt</span><span class="p">{</span>vR<span class="p">}</span>   <span class="k" style="font-weight: 600;">\optOptLine</span><span class="p">{</span>read coordinate of the variant.<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="tex"><span class="nt" style="color: #000080;">\end{optOptTable}</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="tex"><span class="k" style="font-weight: 600;">\optName</span><span class="p">{</span>outSAMattrIHstart<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="tex">  <span class="k" style="font-weight: 600;">\optValue</span><span class="p">{</span>1<span class="p">}</span></span>

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</li>

<li id="8955c7301dc01c7f9b2a350f2aee6066e91f8f83">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#8955c7301dc01c7f9b2a350f2aee6066e91f8f83"><strong>extras/docker/Dockerfile</strong></a>

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

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">MAINTAINER</span><span class="s" style="color: #d14;"> dobin@cshl.edu</span></span>

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> STAR_VERSION=2.7.5<span class="idiff left right">a</span></span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">ARG</span><span class="s" style="color: #d14;"> STAR_VERSION=2.7.5<span class="idiff left right">c</span></span></span>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PACKAGES gcc g++ make wget zlib1g-dev unzip</span></span>

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

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<li id="165858b6de35f6f7c794dcfe8e28a97119310ec8">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#165858b6de35f6f7c794dcfe8e28a97119310ec8"><strong>source/ErrorWarning.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "TimeFunctions.h"</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GlobalVariables.h"</span></span>

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">exitWithError</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">messageOut</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut1</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">errorInt</span><span class="p">,</span> <span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">P</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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">exitWithError</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">messageOut</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut1</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">errorInt</span><span class="p">,</span> <span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">P</span><span class="p">)</span></span>

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

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

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

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">runThreadN</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> </span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp">        <span class="n" style="color: #333;">pthread_mutex_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_threadChunks</span><span class="p">.</span><span class="n" style="color: #333;">mutexError</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">time_t</span> <span class="n" style="color: #333;">timeCurrent</span><span class="p">;</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp">    <span class="n" style="color: #333;">time</span><span class="p">(</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">timeCurrent</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">runThreadN</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">pthread_mutex_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_threadChunks</span><span class="p">.</span><span class="n" style="color: #333;">mutexError</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">streamOut1</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp">        <span class="n" style="color: #333;">streamOut1</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;">messageOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">timeMonthDayTime</span><span class="p">(</span><span class="n" style="color: #333;">timeCurrent</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" ...... FATAL ERROR, exiting</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;">flush</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp">    <span class="p">};</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,14 +22,16 @@ void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2,</td>

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

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

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

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

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

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">warningMessage</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">messageOut</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut1</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut2</span><span class="p">,</span> <span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">P</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="idiff left">    </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">time_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">timeCurrent</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp">    <span class="n" style="color: #333;"><span class="idiff left">time</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">timeCurrent</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">P</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">runThreadN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span></span> <span class="n" style="color: #333;">pthread_mutex_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_threadChunks</span><span class="p">.</span><span class="n" style="color: #333;">mutexError</span><span class="p">);</span></span>

</pre>

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

</td>

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

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">warningMessage</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">messageOut</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut1</span><span class="p">,</span> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamOut2</span><span class="p">,</span> <span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">P</span><span class="p">)</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="p"><span class="idiff left right">{</span></span></span>

</pre>

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

</td>

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

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">P</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">runThreadN</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">    <span class="idiff left right">   </span> <span class="n" style="color: #333;">pthread_mutex_lock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_threadChunks</span><span class="p">.</span><span class="n" style="color: #333;">mutexError</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">streamOut1</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp">        <span class="n" style="color: #333;">streamOut1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left">timeMonthDayTime</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">timeCurrent</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff right">\t</span></span><span class="s" style="color: #d14;">WARNING: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">messageOut</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">        <span class="n" style="color: #333;">streamOut1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;"><span class="idiff left right">"!!!!! </span>WARNING: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">messageOut</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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

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

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

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">streamOut2</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp">        <span class="n" style="color: #333;">streamOut2</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left">timeMonthDayTime</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">timeCurrent</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff right">\t</span></span><span class="s" style="color: #d14;">WARNING: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">messageOut</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">        <span class="n" style="color: #333;">streamOut2</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;"><span class="idiff left right">"!!!!! </span>WARNING: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">messageOut</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="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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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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

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

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="33" 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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="p">};</span></span></pre>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">runThreadN</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> </span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">        <span class="n" style="color: #333;">pthread_mutex_unlock</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_threadChunks</span><span class="p">.</span><span class="n" style="color: #333;">mutexError</span><span class="p">);</span>    </span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="p">};</span></span></pre>

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<br>

</li>

<li id="91be571d30070624a6131ee976f3c342107c4696">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#91be571d30070624a6131ee976f3c342107c4696"><strong>source/GTF.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ GTF::GTF(Genome &genome, Parameters &P, const string &dirOut, SjdbClass &sjdbLoc</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFchrPrefix</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="n" style="color: #333;">chr1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFchrPrefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chr1</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">chrNameIndex</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">chr1</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//chr not in Genome</span></span>

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<td class="diff-line-num old old_line" data-linenumber="74" 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="74" 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="LC74" class="line" lang="cpp">                <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"WARNING: while processing <span class="idiff left right">pGe.</span>sjdbGTFfile="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFfile</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": chromosome '"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">chr1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"' not found in Genome fasta files for line:</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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<td class="diff-line-num new old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">                <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"WARNING: while processing sjdbGTFfile="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFfile</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">": chromosome '"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">chr1</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"' not found in Genome fasta files for line:</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="LC75" class="line" lang="cpp">                <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">oneLine</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;">flush</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//do not process exons/transcripts on missing chromosomes</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp">            <span class="p">};</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +79,12 @@ GTF::GTF(Genome &genome, Parameters &P, const string &dirOut, SjdbClass &sjdbLoc</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">            <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">ex1</span><span class="p">,</span><span class="n" style="color: #333;">ex2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp">            <span class="n" style="color: #333;">oneLineStream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ex1</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ex2</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ddd2</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">str1</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ddd2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//read all fields except the last</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">ex2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">[</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">chrNameIndex</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]]</span> <span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">                   <span class="n" style="color: #333;">warningMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"while processing sjdbGTFfile="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", line:</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;">oneLine</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;"> exon end = "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">ex2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span>  \</span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">                                          <span class="s" style="color: #d14;">" is larger than the chromosome "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chr1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" length = "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">[</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">chrNameIndex</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]]</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" , will skip this exon</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="LC85" class="line" lang="cpp">                                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC86" 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="LC87" class="line" lang="cpp">            <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">            </span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">oneLine1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">            <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">oneLineStream</span><span class="p">,</span> <span class="n" style="color: #333;">oneLine1</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//get the last field     </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,7 +158,11 @@ GTF::GTF(Genome &genome, Parameters &P, const string &dirOut, SjdbClass &sjdbLoc</td>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exonN</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp">        <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC160" class="line" lang="cpp">        <span class="n" style="color: #333;">errOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Fatal INPUT FILE error, no valid ""exon"" lines in the GTF file: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">sjdbGTFfile</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="LC155" class="line" lang="cpp">        <span class="n" style="color: #333;">errOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Solution: check the formatting of the GTF file. <span class="idiff left right">Most</span> likely cause is the difference in chromosome naming between GTF and FASTA file.</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="LC161" class="line" lang="cpp">        <span class="n" style="color: #333;">errOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Solution: check the formatting of the GTF file. <span class="idiff left right">One</span> likely cause is the difference in chromosome naming between GTF and FASTA file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">        <span class="n" style="color: #333;">exitWithError</span><span class="p">(</span><span class="n" style="color: #333;">errOut</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">EXIT_CODE_INPUT_FILES</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp">    </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">    <span class="n" style="color: #333;">exonLoci</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">exonN</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//previous exonLoci.size() was an estimate, need to reszie to the actual value</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"><span class="p">};</span></span></pre>

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<br>

</li>

<li id="f4eb1c9c89d8a6664c03d29afd21f3104689a8d9">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#f4eb1c9c89d8a6664c03d29afd21f3104689a8d9"><strong>source/Genome_genomeGenerate.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="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +142,14 @@ void Genome::genomeGenerate() {</td>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">    <span class="n" style="color: #333;">nGenome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genomeScanFastaFiles</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//first scan the fasta file to find all the sizes</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">    <span class="n" style="color: #333;">genomeSequenceAllocate</span><span class="p">(</span><span class="n" style="color: #333;">nGenome</span><span class="p">,</span> <span class="n" style="color: #333;">nG1alloc</span><span class="p">,</span> <span class="n" style="color: #333;">G</span><span class="p">,</span> <span class="n" style="color: #333;">G1</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); 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="144" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC144" class="line" lang="cpp">    <span class="n" style="color: #333;">genomeScanFastaFiles</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">,</span><span class="n" style="color: #333;">G</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span>    <span class="c1" style="color: #998; font-style: italic;">//load the genome sequence</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" 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="145" 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="LC145" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_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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<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>

</pre>

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<td class="diff-line-num new old_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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<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="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">nGenomeTrue</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<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="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cl</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">chrLength</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">          <span class="n" style="color: #333;">nGenomeTrue</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cl</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Genome sequence total length = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nGenomeTrue</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>

</pre>

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Genome size with padding = "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nGenome</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>

</pre>

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

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//consensusSequence(); //replace with consensus allele </span></span>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

147

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">    <span class="n" style="color: #333;">SjdbClass</span> <span class="n" style="color: #333;">sjdbLoci</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//will be filled in transcriptGeneSJ below</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(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">@@ -157,10 +164,10 @@ void Genome::genomeGenerate() {</td>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp">    <span class="n" style="color: #333;">sjdbLoadFromFiles</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">,</span><span class="n" style="color: #333;">sjdbLoci</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//this will not be transformed. TODO prevent this parameter combination</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<td class="diff-line-num new_line old" data-linenumber="167" 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="LC160" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gSAindexNbases</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">nGenome</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gSAindexNbases</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">nGenome<span class="idiff left right">True</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">        <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">warnOut</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp">        <span class="n" style="color: #333;">warnOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"--genomeSAindexNbases "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gSAindexNbases</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" is too large for the genome size="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nGenome</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp">        <span class="n" style="color: #333;">warnOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">nGenome</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">        <span class="n" style="color: #333;">warnOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"--genomeSAindexNbases "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gSAindexNbases</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" is too large for the genome size="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nGenome<span class="idiff left right">True</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp">        <span class="n" style="color: #333;">warnOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">nGenome<span class="idiff left right">True</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp">        <span class="n" style="color: #333;">warningMessage</span><span class="p">(</span><span class="n" style="color: #333;">warnOut</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span><span class="n" style="color: #333;">P</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">    <span class="p">};</span>    </span>

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC173" 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">@@ -183,7 +190,7 @@ void Genome::genomeGenerate() {</td>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// GstrandBit</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp">    <span class="n" style="color: #333;">GstrandBit</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="p">)</span> <span class="n" style="color: #333;">floor</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">nGenome</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">limitSjdbInsertNsj</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sjdbLength</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//GstrandBit uses P.limitSjdbInsertNsj even if no insertion requested, in case it will be requested at the mapping stage</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">GstrandBit</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="n" style="color: #333;">GstrandBit</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">32</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//TODO: should not this be 31? Need to test for small genomes. TODO: use simple access function for SA</span></span>

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<td class="diff-line-num new_line old" data-linenumber="193" 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="LC186" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Estimated genome size="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">nGenome</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">limitSjdbInsertNsj</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sjdbLength</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;">nGenome</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;">P</span><span class="p">.</span><span class="n" style="color: #333;">limitSjdbInsertNsj</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sjdbLength</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="LC193" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Estimated genome size<span class="idiff left right"> with padding and SJs: total=genome+SJ</span>="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">nGenome</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">limitSjdbInsertNsj</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sjdbLength</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;">nGenome</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;">P</span><span class="p">.</span><span class="n" style="color: #333;">limitSjdbInsertNsj</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sjdbLength</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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<td class="diff-line-num new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp">    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"GstrandBit="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">GstrandBit</span><span class="p">)</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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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp">    <span class="n" style="color: #333;">GstrandMask</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="mi" style="color: #099;">1LLU</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">GstrandBit</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp">    <span class="n" style="color: #333;">SA</span><span class="p">.</span><span class="n" style="color: #333;">defineBits</span><span class="p">(</span><span class="n" style="color: #333;">GstrandBit</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">nSA</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="a0b6c92785c5892df94b89d21ead0dc460541d74">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#a0b6c92785c5892df94b89d21ead0dc460541d74"><strong>source/IncludeDefine.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,12 +117,13 @@ typedef uint8_t uint8;</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BAM_CIGAR_X 8</span></span>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC118" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC119" class="line" lang="cpp"></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BAM_ATTR_MaxSize 10000</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="123" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC123" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined COMPILE_FOR_LONG_READS</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); 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="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">    <span class="cp" style="color: #999; font-weight: 600;">#define MAX_N_EXONS 1000</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" 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="125" 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="LC122" class="line" lang="cpp">    <span class="cp" style="color: #999; font-weight: 600;">#define BAM_ATTR_MaxSize 10000</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); 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="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">    <span class="cp" style="color: #999; font-weight: 600;">#define MAX_N_EXONS 20</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="127" 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="LC125" class="line" lang="cpp">    <span class="cp" style="color: #999; font-weight: 600;">#define BAM_ATTR_MaxSize 1000</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); 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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC129" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//input reads</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -151,6 +152,7 @@ typedef uint8_t uint8;</td>

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

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define EXIT_CODE_FILE_OPEN 109</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define EXIT_CODE_FILE_WRITE 110</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define EXIT_CODE_INCONSISTENT_DATA 111</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define EXIT_CODE_FIFO 112</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//cleaned-end</span></span>

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<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="6ae9e88712056a2abd55911f4d3a7d8b8145819c">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#6ae9e88712056a2abd55911f4d3a7d8b8145819c"><strong>source/Makefile</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ CFLAGS ?= -pipe -Wall -Wextra -O3</td>

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

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<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="make"><span class="c" style="color: #998; font-style: italic;"># Unconditionally set essential flags and optimization options</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS_common</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nv" style="color: #008080;">$(COMPTIMEPLACE)</span></span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS_main</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nv" style="color: #008080;">$(CXXFLAGS_common)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS_gdb</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-O</span> <span class="nt" style="color: #000080;">-g3</span> <span class="nv" style="color: #008080;">$(CXXFLAGS_common)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS_gdb</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-O<span class="idiff left right">0</span></span> <span class="nt" style="color: #000080;">-g3</span> <span class="nv" style="color: #008080;">$(CXXFLAGS_common)</span></span>

</pre>

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31

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31

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">##########################################################################################################</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">

33

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

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">OBJECTS</span> <span class="o" style="font-weight: 600;">=</span> soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o <span class="se" style="color: #d14;">\</span></span>

</pre>

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<br>

</li>

<li id="6e7e9199db44be8b0f606c7c21db10763fc8b0eb">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#6e7e9199db44be8b0f606c7c21db10763fc8b0eb"><strong>source/Parameters.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1339" style="width: 35px; color: rgba(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="1339" style="width: 35px; color: rgba(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">@@ -1339,6 +1339,7 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="cpp">    <span class="p">};</span></span>

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<td class="diff-line-num new_line" data-linenumber="1340" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1340" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1341

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<td class="diff-line-num new_line" data-linenumber="1341" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1341" class="line" lang="cpp">    <span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">nBasesMax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="1342" style="width: 35px; color: rgba(0,0,0,0.3); 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="1342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="cpp">    <span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">concordantPair</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="LC1343" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">nBasesMax</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//allow ends protrusion</span></span>

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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"ConcordantPair"</span><span class="p">)</span> <span class="p">{</span></span>

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1344

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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="cpp">            <span class="n" style="color: #333;">alignEndsProtrude</span><span class="p">.</span><span class="n" style="color: #333;">concordantPair</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<br>

</li>

<li id="bf27f52254916f0127a15b2aa4242b8679bb9815">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#bf27f52254916f0127a15b2aa4242b8679bb9815"><strong>source/ParametersSolo.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,13 +137,21 @@ void ParametersSolo::initialize(Parameters *pPin)</td>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">        <span class="n" style="color: #333;">exitWithError</span><span class="p">(</span><span class="n" style="color: #333;">errOut</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">(),</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">EXIT_CODE_PARAMETER</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pP</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>

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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;">featureYes</span><span class="p">[</span><span class="n" style="color: #333;">SoloFeatureTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gene</span><span class="p">])</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="141" 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="LC141" class="line" lang="cpp">        <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="140" 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="LC142" class="line" lang="cpp">        <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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;">featureYes</span><span class="p">[</span><span class="n" style="color: #333;">SoloFeatureTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Velocyto</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">SoloTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SmartSeq</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"EXITING because of fatal PARAMETERS error: --soloFeatures Velocyto is presently not compatible with --soloType SmartSeq .</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="LC142" class="line" lang="cpp">        <span class="n" style="color: #333;">errOut</span>       <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"SOLUTION: re-run without --soloFeatures Velocyto ."</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">        <span class="n" style="color: #333;">exitWithError</span><span class="p">(</span><span class="n" style="color: #333;">errOut</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">EXIT_CODE_PARAMETER</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pP</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC144" class="line" lang="cpp">    <span class="p">};</span></span>

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<td class="diff-line-num old old_line" data-linenumber="144" 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="145" 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="LC144" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">featureYes</span><span class="p">[</span><span class="n" style="color: #333;">SoloFeatureTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GeneFull</span><span class="p">])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">        <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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146

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp">        <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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

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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">SoloTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CB_samTagOut</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//gene quantification is needed</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">featureYes</span><span class="p">[</span><span class="n" style="color: #333;">SoloFeatureTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gene</span><span class="p">])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">            <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp">            <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">featureYes</span><span class="p">[</span><span class="n" style="color: #333;">SoloFeatureTypes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GeneFull</span><span class="p">])</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp">            <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp">            <span class="n" style="color: #333;">pP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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="LC154" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">    </span>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">////////////////////////////////////////////umiDedup</span></span>

</pre>

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<br>

</li>

<li id="b6bbf0242e5e8b3ccfc1f5b5a8ccf033fb5ae809">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#b6bbf0242e5e8b3ccfc1f5b5a8ccf033fb5ae809"><strong>source/Parameters_openReadsFiles.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,13 @@ void Parameters::openReadsFiles()</td>

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27

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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;">sysCom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outFileTmp</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"tmp.fifo.read"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">imate</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp">            <span class="n" style="color: #333;">readFilesInTmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">sysCom</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">());</span></span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">            <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">readFilesInTmp</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp">            <span class="n" style="color: #333;">mkfifo</span><span class="p">(</span><span class="n" style="color: #333;">readFilesInTmp</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">S_IRUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">S_IWUSR</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mkfifo</span><span class="p">(</span><span class="n" style="color: #333;">readFilesInTmp</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">S_IRUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">S_IWUSR</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">                <span class="n" style="color: #333;">exitWithError</span><span class="p">(</span><span class="s" style="color: #d14;">"Exiting because of *FATAL ERROR*: could not create FIFO file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">readFilesInTmp</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">)</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>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">                            <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"SOLUTION: check the if run directory supports FIFO files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">                            <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), "</span></span>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"re-run on a Linux partition, or point --outTmpDir to a Linux partition.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">                            <span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">EXIT_CODE_FIFO</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

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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>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</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;">   Input read files for mate "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">imate</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="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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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<br>

</li>

<li id="b7114790c4e1e6b022e2111cc5b7c713050c42a0">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#b7114790c4e1e6b022e2111cc5b7c713050c42a0"><strong>source/Parameters_readSAMheader.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,13 @@ void Parameters::readSAMheader(const string readFilesCommandString, const vector</td>

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

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

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmpFifo</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outFileTmp</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"tmp.fifo.header"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp">    <span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">tmpFifo</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<td class="diff-line-num old old_line" data-linenumber="21" 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="21" 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="LC21" class="line" lang="cpp">    <span class="n" style="color: #333;">mkfifo</span><span class="p">(</span><span class="n" style="color: #333;">tmpFifo</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">S_IRUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">S_IWUSR</span> <span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mkfifo</span><span class="p">(</span><span class="n" style="color: #333;">tmpFifo</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">S_IRUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">S_IWUSR</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">        <span class="n" style="color: #333;">exitWithError</span><span class="p">(</span><span class="s" style="color: #d14;">"Exiting because of *FATAL ERROR*: could not create FIFO file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpFifo</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>

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

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">                      <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"SOLUTION: check the if run directory supports FIFO files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">                      <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), "</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">                      <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"re-run on a Linux partition, or point --outTmpDir to a Linux partition.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">                      <span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span><span class="p">,</span> <span class="n" style="color: #333;">EXIT_CODE_FIFO</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>

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

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

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

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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>

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

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">    <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">tmpFifoIn</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">readFilesNames</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<br>

</li>

<li id="7245d12cb1ad9b44f08daa0ab3e702d4bed39531">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#7245d12cb1ad9b44f08daa0ab3e702d4bed39531"><strong>source/ReadAlignChunk_processChunks.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">@@ -5,6 +5,12 @@</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SequenceFuns.h"</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GlobalVariables.h"</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">removeStringEndControl</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>

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

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//removes control character (including space) from the end of the string</span></span>

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

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

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">())</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">33</span><span class="p">)</span></span>

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

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

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp">        <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>

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

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12

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

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

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

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

8

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReadAlignChunk</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">processChunks</span><span class="p">()</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//read-map-write chunks</span></span>

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

9

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp">    <span class="n" style="color: #333;">noReadsLeft</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//true if there no more reads left in the file</span></span>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">newFile</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//new file marker in the input stream</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +85,7 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFilterBySJoutStage</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//not the 2nd stage of the 2-stage mapping, read ID from the 1st read</span></span>

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">                        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">readID</span><span class="p">;</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">                        <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">readID</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">                        <span class="n" style="color: #333;">removeStringEndControl</span><span class="p">(</span><span class="n" style="color: #333;">readID</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMreadIDnumber</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">                            <span class="n" style="color: #333;">readID</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">iReadAll</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">                        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -87,9 +94,11 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">peek</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//2nd field exists</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp">                            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">field2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp">                            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">field2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" 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="97" 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="LC90" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">field2</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">field2</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="sc" style="color: #d14;"><span class="idiff">':'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field2</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="sc" style="color: #d14;"><span class="idiff">'Y'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field2</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">':'</span> <span class="p">)</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">field2</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">field2</span><span class="p"><span class="idiff left">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="sc" style="color: #d14;"><span class="idiff">':'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field2</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="sc" style="color: #d14;"><span class="idiff">'Y'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">field2</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff right">]</span></span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">':'</span> <span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC98" class="line" lang="cpp">                                <span class="n" style="color: #333;">passFilterIllumina</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'Y'</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp">                        <span class="p">};</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">                        </span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">                        <span class="c1" style="color: #998; font-style: italic;">//add extra information to readID line</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">                        <span class="n" style="color: #333;">readID</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">iReadAll</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="sc" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">passFilterIllumina</span><span class="o" style="font-weight: 600;">+</span><span class="sc" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readFilesIndex</span><span class="p">);</span></span>

</pre>

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94

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">                        <span class="c1" style="color: #998; font-style: italic;">//ignore the rest of the read name for both mates</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,6 +108,7 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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99

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeReadYes</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//record barcode sequence</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">                            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">                            <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeRead</span><span class="p">],</span><span class="n" style="color: #333;">seq1</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">                            <span class="n" style="color: #333;">removeStringEndControl</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">bL</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); 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="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">bL</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp">                                                                  <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,6 +124,7 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">                            <span class="n" style="color: #333;">readID</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">                            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeRead</span><span class="p">].</span><span class="n" style="color: #333;">ignore</span><span class="p">(</span><span class="n" style="color: #333;">DEF_readNameSeqLengthMax</span><span class="p">,</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//skip to the end of 3rd ("+") line</span></span>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">                            <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeRead</span><span class="p">],</span><span class="n" style="color: #333;">seq1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//read qualities</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">                            <span class="n" style="color: #333;">removeStringEndControl</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">                            <span class="n" style="color: #333;">readID</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); 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="129" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC129" class="line" lang="cpp">                            <span class="n" style="color: #333;">g_statsAll</span><span class="p">.</span><span class="n" style="color: #333;">qualHistCalc</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeStart</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeEnd</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeEnd</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">barcodeStart</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp">                        <span class="p">};</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,12 +138,19 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">//copy 3 (4 for stage 2) lines: sequence, dummy, quality</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">imate</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">imate</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmates</span><span class="p">;</span> <span class="n" style="color: #333;">imate</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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129

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iline</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFilterBySJoutStage</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">1</span><span class="p">);</span><span class="n" style="color: #333;">iline</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</span><span class="p">;</span><span class="n" style="color: #333;">iline</span><span class="o" style="font-weight: 600;">++</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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">                            <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">origChunkStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">];</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">                            </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC143" class="line" lang="cpp">                            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">],</span> <span class="n" style="color: #333;">DEF_readNameSeqLengthMax</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="144" 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="LC131" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">();</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">//this includes the final \n</span></span>

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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>

</pre>

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

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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;">if</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">][</span><span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">33</span> <span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//remove control char at the end if present</span></span>

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

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">                                <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre>

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

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp">                            </span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">][</span><span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">                            </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iline</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFilterBySJoutStage</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="153" 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="LC135" class="line" lang="cpp">                                <span class="n" style="color: #333;">g_statsAll</span><span class="p">.</span><span class="n" style="color: #333;">qualHistCalc</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">,</span> <span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">chunkInSizeBytesTotal</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">P</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inOut</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">readIn</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">gcount</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">P</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">inOut</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">readIn</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">gcount</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp">                                <span class="n" style="color: #333;">g_statsAll</span><span class="p">.</span><span class="n" style="color: #333;">qualHistCalc</span><span class="p">(</span><span class="n" style="color: #333;">imate</span><span class="p">,</span> <span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">origChunkStart</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chunkInSizeBytesTotal</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">origChunkStart</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">                            <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">                        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">                    <span class="p">};</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -151,18 +169,20 @@ void ReadAlignChunk::processChunks() {//read-map-write chunks</td>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">                            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">ignore</span><span class="p">(</span><span class="n" style="color: #333;">DEF_readNameSeqLengthMax</span><span class="p">,</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">],</span> <span class="s" style="color: #d14;">" %llu %c %i </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">iReadAll</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readFilesIndex</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">                        <span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//                         else {//2nd stage of 2-stage mapping</span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//                         read index and file index are already recorded with the read name, simply copy it</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//                         P.inOut->readIn[imate].getline(chunkIn[imate] + chunkInSizeBytesTotal[imate], DEF_readNameSeqLengthMax+1 );</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//                         };</span></span>

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

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

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

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp">                        <span class="c1" style="color: #998; font-style: italic;">//read multi-line fasta</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp">                        <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" 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">

162

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<td class="diff-line-num new_line old" data-linenumber="176" 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="LC162" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'@'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'>'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//read multi-line fasta</span></span></span>

</pre>

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

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

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'@'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'>'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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<td class="diff-line-num new_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">

177

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp">                            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">],</span> <span class="n" style="color: #333;">DEF_readSeqLengthMax</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" 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">

164

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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//no more input</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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

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

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> </span>

</pre>

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

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

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">                                <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//no more input</span></span>

</pre>

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

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

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">                                </span>

</pre>

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

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

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">                            <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">gcount</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//-1 because \n was counted, bu wee need to remove it</span></span>

</pre>

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

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

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">][</span><span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">33</span> <span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//remove control char at the end if present</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">                                <span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">                            <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">                            </span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp">                            <span class="n" style="color: #333;">nextChar</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">].</span><span class="n" style="color: #333;">peek</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp">                        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp">                        <span class="n" style="color: #333;">chunkIn</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">][</span><span class="n" style="color: #333;">chunkInSizeBytesTotal</span><span class="p">[</span><span class="n" style="color: #333;">imate</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>

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<br>

</li>

<li id="764c3cfc36fad2f293fd356112b8836ea61e0b02">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#764c3cfc36fad2f293fd356112b8836ea61e0b02"><strong>source/ReadAlign_alignBAM.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -374,13 +374,25 @@ int ReadAlign::alignBAM(Transcript const &trOut, uint nTrOut, uint iTrOut, uint</td>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_UY</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp">                        <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">soloRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBar</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">umiQual</span><span class="p">,</span><span class="s" style="color: #d14;">"UY"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_GX</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="378" 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="379" 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="LC378" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneConcordant</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene, and this alignment maps to one gene</span></span>

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<td class="diff-line-num new_line old" data-linenumber="379" 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="LC379" class="line" lang="cpp">                            <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geID</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GX"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">yes</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="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneConcordant</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene, and this alignment maps to one gene</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">                                <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geID</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GX"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC382" 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;">P</span><span class="p">.</span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">yes</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="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp">                                <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geID</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GX"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp">                        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); 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="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC386" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp">                            </span>

</pre>

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381

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<td class="diff-line-num new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_GN</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" 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="389" 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="LC382" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneConcordant</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene, and this alignment maps to one gene</span></span>

</pre>

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383

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<td class="diff-line-num new_line old" data-linenumber="389" 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="LC383" class="line" lang="cpp">                            <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geName</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GN"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">yes</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="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

390

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneConcordant</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene, and this alignment maps to one gene</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp">                                <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geName</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">alignGenes</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GN"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC392" 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;">P</span><span class="p">.</span><span class="n" style="color: #333;">quant</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//only output if read maps to a single gene</span></span>

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<td class="diff-line-num new old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp">                                <span class="n" style="color: #333;">attrN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">bamAttrArrayWrite</span><span class="p">(</span><span class="n" style="color: #333;">chunkTr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geName</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readAnnot</span><span class="p">.</span><span class="n" style="color: #333;">geneFull</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()],</span><span class="s" style="color: #d14;">"GN"</span><span class="p">,</span><span class="n" style="color: #333;">attrOutArray</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">attrN</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp">                        <span class="p">};</span>                           </span>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span>                        </span>

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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC397" class="line" lang="cpp">                        </span>

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<td class="diff-line-num old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_sM</span><span class="p">:</span></span>

</pre>

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<br>

</li>

<li id="4896a67af34962395106d0bd2c41b227ffde5a58">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#4896a67af34962395106d0bd2c41b227ffde5a58"><strong>source/STAR.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,8 +49,7 @@ void usage(int usageType) {</td>

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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">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">                   <span class="n" style="color: #333;">parametersDefault_len</span><span class="p">);</span></span>

</pre>

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50

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50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">    <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"><span class="p">}</span></span>

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

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="p">};</span></span>

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argInN</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argIn</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// If no argument is given, or the first argument is either '-h' or '--help', run usage()</span></span>

</pre>

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<br>

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<li id="8ab4cbdfbf463cf0757c6b325b3b1b4d95720372">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#8ab4cbdfbf463cf0757c6b325b3b1b4d95720372"><strong>source/SoloFeature_collapseUMI.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +89,7 @@ uint32 graphNumberOfConnectedComponents(uint32 N, vector<array<uint32,2>> V, vec</td>

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89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">    </span>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">    <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">nConnComp</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">N</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="92" 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="92" 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="LC92" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodeEdges</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//this node is not connected, no need to check. Save time be<span class="idiff left right">ac</span>use this happens often</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodeEdges</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//this node is not connected, no need to check. Save time be<span class="idiff left right">ca</span>use this happens often</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nConnComp</span><span class="p">;</span></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC94" 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;">nodeColor</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//node not visited</span></span>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nConnComp</span><span class="p">;</span></span>

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<br>

</li>

<li id="e79ceffd8a1458e9765b7ce8380e4e8568543d53">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#e79ceffd8a1458e9765b7ce8380e4e8568543d53"><strong>source/Transcriptome_classifyAlign.cpp</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,11 +22,13 @@ int alignToTranscript(Transcript &aG, uint64 trS1, uint16 exN1, uint32 *exSE1, u</td>

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//distTTS=trLen[tr1]-(gthaG.exons[iab][EX_G]-trS1-exSE1[2*ex1]+exLenCum1[ex1]+aG.exons[iab][EX_L]);</span></span>

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//if trStr1==2: TTS=trLen[tr1]-TTS, TSS=trLen[tr1]-TSS</span></span>

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

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

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

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ex1</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bS</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">eE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">enS</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp">                <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">aG</span><span class="p">.</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span> <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//scan through all blocks of the align</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ex1</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bS</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">eE</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">enS</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span>  <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">aG</span><span class="p">.</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span>  <span class="n" style="color: #333;">iab</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//scan through all blocks of the align</span></span>

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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="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>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp">        <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">bEprev</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bE</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">aG</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iab</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">trS1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//this can happen for PE reads, when the 2nd mate protrudes to the left of the first</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">        <span class="n" style="color: #333;">bS</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">aG</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iab</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">trS1</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//block start</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">        <span class="n" style="color: #333;">bE</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bS</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">aG</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iab</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//block end</span></span>

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

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<li id="46ef577d4524cc6123d3e3cfa053a5ca85c35274">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#46ef577d4524cc6123d3e3cfa053a5ca85c35274"><strong>source/VERSION</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "2.7.5<span class="idiff left right">a_2020-06-29</span>"</span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "2.7.5<span class="idiff left right">c</span>"</span></pre>

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<li id="d1de46dc38c5a41c3a5dc9d20994daf72784ac7d">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#d1de46dc38c5a41c3a5dc9d20994daf72784ac7d"><strong>source/genomeScanFastaFiles.cpp</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,8 @@ uint genomeScanFastaFiles (Parameters &P, char* G, bool flagRun, Genome &mapGen)</td>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">                    <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">chrName1</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">                <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flagRun</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//true length of the chr</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flagRun</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">());</span> <span class="c1" style="color: #998; font-style: italic;">//true length of the chr</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"></span>

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

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//pad the chromosomes to bins boudnaries</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">                    <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">genomeChrBinNbases</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">genomeChrBinNbases</span><span class="p">;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +53,9 @@ uint genomeScanFastaFiles (Parameters &P, char* G, bool flagRun, Genome &mapGen)</td>

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

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flagRun</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">                    <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp">                    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gFastaFiles</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" : chr # "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  </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;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> chrStart: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">N</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;">flush</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">                    <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gFastaFiles</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" : chr # "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span>   \</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">                                            <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  </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;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span>       \</span>

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

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

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//char lines</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">flagRun</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,15 +73,17 @@ uint genomeScanFastaFiles (Parameters &P, char* G, bool flagRun, Genome &mapGen)</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">    <span class="p">};</span></span>

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

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flagRun</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp">        <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">at</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mapGen</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrStart</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//true length of the last chr</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">        <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">back</span></span><span class="p"><span class="idiff right">(</span>));</span> <span class="c1" style="color: #998; font-style: italic;">//true length of the last chr</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC78" class="line" lang="cpp">    <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">genomeChrBinNbases</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">genomeChrBinNbases</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flagRun</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp">        <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">nChrReal</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">        <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">N</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//last chromosome end+1</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">        <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Chromosome sequence lengths: </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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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">nChrReal</span><span class="p">;</span><span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">            <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrNameIndex</span><span class="p">[</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">            <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">inOut</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">logMain</span> <span class="o" style="font-weight: 600;"><<</span>  <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrLength</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</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="LC87" class="line" lang="cpp">        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>

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<br>

</li>

<li id="14e4f2926f46a184cc81f069a1550cb71e369b6d">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#14e4f2926f46a184cc81f069a1550cb71e369b6d"><strong>source/parametersDefault</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -269,26 +269,38 @@ outSAMstrandField               None</td>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext">                                intronMotif ... strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out.</span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext">outSAMattributes                Standard</span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext">    string: a string of desired SAM attributes, in the order desired for the output SAM</span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext">                                <span class="idiff left right">NH HI AS nM NM MD jM jI XS MC ch ... any combination in any order</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">    string: a string of desired SAM attributes, in the order desired for the output SAM<span class="idiff left right">. Tags can be listed in any combination/order.</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">                                <span class="idiff left right">***Presets:</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext">                                None        ... no attributes</span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext">                                Standard    ... NH HI AS nM</span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="plaintext">                                All         ... NH HI AS nM NM MD jM jI MC ch</span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext">                                variation:</span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">                                All         ... NH HI AS nM NM MD jM jI MC ch                                                                    </span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">                                ***Alignment:</span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">                                NH          ... number of loci the reads maps to: =1 for unique mappers, >1 for multimappers. Standard SAM tag.</span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">                                HI          ... multiple alignment index, starts with --outSAMattrIHstart (=1 by default). Standard SAM tag.</span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">                                AS          ... local alignment score, +1/-1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag.</span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">                                nM          ... number of mismatches. For PE reads, sum over two mates.</span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">                                NM          ... edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.</span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">                                MD          ... string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">                                jM          ... intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">                                jI          ... start and end of introns for all junctions (1-based).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">                                XS          ... alignment strand according to --outSAMstrandField.</span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">                                MC          ... mate's CIGAR string. Standard SAM tag.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">                                ch          ... marks all segment of all chimeric alingments for --chimOutType WithinBAM output.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">                                ***Variation:</span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext">                                vA          ... variant allele</span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">                                ha          ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid</span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext">                                vG          ... genomic coordinate of the variant overlapped by the read</span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">                                vG          ... genomic coordinate of the variant overlapped by the read.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext">                                vW          ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --waspOutputMode SAMtag.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext">                                STARsolo:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext">                                CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing</span>

</pre>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">                                ***STARsolo:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">                                CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">                                GX GN       ... gene ID and gene name.                                </span>

</pre>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext">                                CB UB       ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext">                                sM          ... assessment of CB and UMI</span>

</pre>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">                                sS          ... sequence of the entire barcode (CB,UMI,adapter<span class="idiff left right">...)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext">                                sQ          ... quality of the entire barcode</span>

</pre>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">                                <span class="idiff left right">GX GN       ... gene ID and gene name</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">                                <span class="idiff left right">Unsupported/undocumented:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext">                                rB          ... alignment block read/genomic coordinates</span>

</pre>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext">                                vR          ... read coordinate of the variant</span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">                                sM          ... assessment of CB and UMI<span class="idiff left right">.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">                                sS          ... sequence of the entire barcode (CB,UMI,adapter<span class="idiff left right">).</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">                                sQ          ... quality of the entire barcode<span class="idiff left right">.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">                                <span class="idiff left right">***Unsupported/undocumented:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">                                <span class="idiff left right">ha          ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid .                               </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">                                rB          ... alignment block read/genomic coordinates<span class="idiff left right">.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">                                vR          ... read coordinate of the variant<span class="idiff left right">.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext">outSAMattrIHstart               1</span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext">    int>=0:                     start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.</span>

</pre>

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<br>

</li>

<li id="8d3b9ff64d8dd5569149f7e7f75554bcab49ad30">

<a href="https://salsa.debian.org/med-team/rna-star/-/commit/63ea00262b1c169acb719ad4e01b005ef625d0e5#8d3b9ff64d8dd5569149f7e7f75554bcab49ad30"><strong>source/readLoad.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,7 +84,7 @@ int readLoad(istream& readInStream, Parameters& P, uint iMate, uint& Lread, uint</td>

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<pre style="margin: 0;"> <span id="LC84" 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="LC85" class="line" lang="cpp">        <span class="n" style="color: #333;">Lread</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="p">};</span></span>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">convertNucleotidesToNumbers<span class="idiff left right">RemoveControls</span></span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip5pNbases</span><span class="p">[</span><span class="n" style="color: #333;">iMate</span><span class="p">],</span><span class="n" style="color: #333;">SeqNum</span><span class="p">,</span><span class="n" style="color: #333;">Lread</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">convertNucleotidesToNumbers</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip5pNbases</span><span class="p">[</span><span class="n" style="color: #333;">iMate</span><span class="p">],</span><span class="n" style="color: #333;">SeqNum</span><span class="p">,</span><span class="n" style="color: #333;">Lread</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//clip the adapter</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip3pAdapterSeq</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">iMate</span><span class="p">).</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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