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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/rna-star">Debian Med / rna-star</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70">ababb9e7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-02T14:49:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.7.6a+dfsg</pre>
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<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#fb1b39277cfb15327cea71551d0bbf7643e216f4">
RELEASEnotes.md
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<li class="file-stats">
<a href="#1d6ebb42152a3125296c8f3df8bc34651da72448">
doc/STARmanual.pdf
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<li class="file-stats">
<a href="#5a5668ccb427693fe0e7ea2e054229206cb91b0a">
extras/doc-latex/STARmanual.tex
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<li class="file-stats">
<a href="#8955c7301dc01c7f9b2a350f2aee6066e91f8f83">
extras/docker/Dockerfile
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<li class="file-stats">
<a href="#05aaea645830f1788b63f5f6c2c90809c8837dee">
source/BAMfunctions.cpp
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<li class="file-stats">
<a href="#17ef85fa9dc8f604b874c27ab2bc5d31a69f0d6d">
source/ChimericAlign.cpp
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<li class="file-stats">
<a href="#a6ffa0e1a002e87767829734d1828c550173c14f">
source/ChimericAlign.h
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source/ChimericAlign_chimericBAMoutput.cpp
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<a href="#40b7d10e4645dc6ae30e5830f3b8abe35c537374">
source/ChimericDetection.h
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<a href="#e6c66b50a9609f09ee3fe8ac72c75014ae38c1ff">
source/ChimericDetection_chimericDetectionMult.cpp
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<a href="#6ae9e88712056a2abd55911f4d3a7d8b8145819c">
source/Makefile
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<a href="#6e7e9199db44be8b0f606c7c21db10763fc8b0eb">
source/Parameters.cpp
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<a href="#09b38547a28087b813616bd2a7334493c3862c48">
source/Parameters.h
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<li class="file-stats">
<a href="#f09ea75b8243d42eee54c10d49465997ac00609f">
source/ParametersChimeric_initialize.cpp
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source/Parameters_samAttributes.cpp
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<a href="#238ae46f3e2ae6c05a1eca3f159a54222230394e">
source/ReadAlign.h
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<a href="#0f351bd6f52ff0c9ab03a4771ab917025e709afc">
source/ReadAlignChunk.cpp
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<a href="#764c3cfc36fad2f293fd356112b8836ea61e0b02">
source/ReadAlign_alignBAM.cpp
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<li class="file-stats">
<a href="#af060c7d950c0018c9102e5f40dcb6ce74317aa8">
source/ReadAlign_chimericDetection.cpp
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<li class="file-stats">
<a href="#e567212bd90532effae5cceb340251e161d1e96e">
source/ReadAlign_chimericDetectionOldOutput.cpp
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<a href="#32c87d85b8e6a7f392241db417a7cd034f3e79d7">
source/ReadAlign_chimericDetectionPEmerged.cpp
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<a href="#38255560373004439a41922897da553297a784d2">
source/ReadAlign_outputAlignments.cpp
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<li class="file-stats">
<a href="#d938845d26281b751fbd64471e18f13e3c550aa8">
source/ReadAlign_outputTranscriptSAM.cpp
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<a href="#188667251bde9bacea8550ecde93b515b078a8a4">
source/ReadAlign_peOverlapMergeMap.cpp
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<li class="file-stats">
<a href="#2ce04271e5214fcd449bb4917e94be04695c6534">
source/SoloFeature_cellFiltering.cpp
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<a href="#afd85a07c3f509b173703f2140b578a707ada9e6">
source/Transcript.h
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<li class="file-stats">
<a href="#eef122fda3a846cd84614a07011c0a84a375639b">
source/Transcript_alignScore.cpp
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<li class="file-stats">
<a href="#46ef577d4524cc6123d3e3cfa053a5ca85c35274">
source/VERSION
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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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 2.7.6a --- 2020/09/19</span></span>
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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">
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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>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Major new feature:**</span></span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Output multimapping chimeric alignments in BAM format using</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">```</span><span class="nl">--chimMultimapNmax N>1 --chimOutType WithinBAM --outSAMtype BAM Unsorted [and/or] SortedByCoordinate```</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="sb" style="color: #d14;">Many thanks to Sebastian @suhrig who implemented this feature!</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="sb" style="color: #d14;">More detailed description from Sebastian in PR #802.</span></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="markdown"></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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="sb" style="color: #d14;">**Minor features and bug fixes:**</span></span>
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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="markdown"><span class="sb" style="color: #d14;">* Issue #1008: fixed the problem with Unmapped.out.mate? output for --soloType CB_samTagOut output.</span></span>
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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="sb" style="color: #d14;">* PR # 1012: fixed the bug with --soloCellFiltering TopCells option.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="sb" style="color: #d14;">* Issue #786: fixed the bug causing the *Different SJ motifs problem* for overlapping mates.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="sb" style="color: #d14;">* Issue #945: GX/GN can be output for all --soloType, as well as for non-solo runs.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;">STAR 2.7.5c --- 2020/08/16</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;">==========================</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="sb" style="color: #d14;">Bug-fix release.</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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>
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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>
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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>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">wget https://github.com/alexdobin/STAR/archive/2.7.<span class="idiff left right">5c</span>.tar.gz</span>
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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.<span class="idiff left right">5c</span>.tar.gz</span>
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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.<span class="idiff left right">5c</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">wget https://github.com/alexdobin/STAR/archive/2.7.<span class="idiff left right">6a</span>.tar.gz</span>
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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.<span class="idiff left right">6a</span>.tar.gz</span>
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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.<span class="idiff left right">6a</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Alternatively, get STAR source using git</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">git clone https://github.com/alexdobin/STAR.git</span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#fb1b39277cfb15327cea71551d0bbf7643e216f4"><strong>RELEASEnotes.md</strong></a>
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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 2.7.6a --- 2020/09/19</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Major new feature:**</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Output multimapping chimeric alignments in BAM format using</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">```</span><span class="nl">--chimMultimapNmax N>1 --chimOutType WithinBAM --outSAMtype BAM Unsorted [and/or] SortedByCoordinate```</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="sb" style="color: #d14;">Many thanks to Sebastian @suhrig who implemented this feature!</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="sb" style="color: #d14;">More detailed description from Sebastian in PR #802.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="sb" style="color: #d14;">STAR 2.7.5a 2020/06/16</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #d14;">======================</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;">**Major new features: </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">@@ -34,7 +34,7 @@</td>
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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.<span class="idiff left right">5c</span><span class="p">}</span></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.<span class="idiff left right">6a</span><span class="p">}</span></span>
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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>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="tex">dobin@cshl.edu<span class="p">}</span></span>
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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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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#8955c7301dc01c7f9b2a350f2aee6066e91f8f83"><strong>extras/docker/Dockerfile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ FROM debian:stable-slim</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.<span class="idiff left right">5c</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.<span class="idiff left right">6a</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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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#05aaea645830f1788b63f5f6c2c90809c8837dee"><strong>source/BAMfunctions.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">@@ -59,9 +59,10 @@ int bam_read1_fromArray(char *bamChar, bam1_t *b) //modified from samtools bam_r</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_data</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l_data</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l_data</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">kroundup32</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_data</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_data</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" 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;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// no need to realloc b->data, because it is overwritten later with bamChar</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// b->data = (uint8_t*)realloc(b->data, b->m_data);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if (!b->data)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// return -4;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// // if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// // //b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#17ef85fa9dc8f604b874c27ab2bc5d31a69f0d6d"><strong>source/ChimericAlign.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ChimericAlign.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="n" style="color: #333;">ChimericAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChimericAlign</span><span class="p">(</span><span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seg1in</span><span class="p">,</span> <span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seg2in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimScoreIn</span><span class="p">,</span> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genomeIn</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RAin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seg1</span><span class="p">(</span><span class="n" style="color: #333;">seg1in</span><span class="p">),</span> <span class="n" style="color: #333;">seg2</span><span class="p">(</span><span class="n" style="color: #333;">seg2in</span><span class="p">),</span><span class="n" style="color: #333;">chimScore</span><span class="p">(</span><span class="n" style="color: #333;">chimScoreIn</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">P</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seg1in</span></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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pCh</span></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">pCh</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </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">genomeIn</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RA</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">RAi</span>n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seg1</span><span class="p">(</span><span class="n" style="color: #333;">seg1in</span><span class="p">),</span> <span class="n" style="color: #333;">seg2</span><span class="p">(</span><span class="n" style="color: #333;">seg2in</span><span class="p">),</span><span class="n" style="color: #333;">chimScore</span><span class="p">(</span><span class="n" style="color: #333;">chimScoreIn</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">RA</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">RAin</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">seg1in</span></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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pCh</span></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">pCh</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </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 right">genomeI</span>n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"> <span class="n" style="color: #333;">stitchingDone</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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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">al1</span><span class="o" style="font-weight: 600;">=&</span><span class="n" style="color: #333;">seg1</span><span class="p">.</span><span class="n" style="color: #333;">align</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">@@ -24,16 +24,17 @@ class ChimericAlign</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">ChimericAlign</span><span class="p">(</span><span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seg1in</span><span class="p">,</span> <span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seg2in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimScoreIn</span><span class="p">,</span> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genomeIn</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RAin</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//allocate</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">chimericJunctionOutput</span><span class="p">(</span><span class="n" style="color: #333;">fstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outStream</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxNonChimAlignScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">PEmerged_flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimScoreBest</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxPossibleAlignScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">chimericBAMoutput</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">al2</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isBestChimAlign</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">chimericStitching</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;">genSeq</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;">Read1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chimericCheck</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stitchingDone</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <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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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">ParametersChimeric</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pCh</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mapGen</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;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#30ab53827d7d7caed59d72d5bb914a74c2e6f333"><strong>source/ChimericAlign_chimericBAMoutput.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ChimericAlign.h"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ReadAlign.h"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BAMfunctions.h"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>
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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 <vector></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ChimericAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericBAMoutput</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">al2</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isBestChimAlign</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Transcript</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">trChim</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</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;">al1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</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="n" style="color: #333;">al2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimRepresent</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">999</span><span class="p">,</span> <span class="n" style="color: #333;">chimType</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="LC14" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</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;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</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;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</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;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 has both mates</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</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="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</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="LC17" 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;">trChim</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="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</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="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</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="n" style="color: #333;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr1 has both mates</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</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="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</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="LC20" 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;">trChim</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;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</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="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 and tr1 are single different mates</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</span> <span class="o" style="font-weight: 600;">=</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="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" 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;">//two chimeric segments are on the same mate - this can only happen for single-end reads</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</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;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trChim</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="n" style="color: #333;">maxScore</span><span class="p">)</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>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignType</span><span class="p">,</span> <span class="n" style="color: #333;">bamN</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;">bamIsuppl</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;">bamIrepr</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="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">bamBytesTotal</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//estimate of the total size of all bam records, for output buffering</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span><span class="n" style="color: #333;">mateStart</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">itr</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;">itr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">itr</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;">//generate bam for all chimeric pieces</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">isBestChimAlign</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimType</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;">//PE, encompassing</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Chr</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;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" 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;">//spanning chimeric alignment, could be PE or SE</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">mateChr</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;">mateStart</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;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//no need fot mate info unless this is the supplementary alignment</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimRepresent</span><span class="o" style="font-weight: 600;">==</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;">itr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">10</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//this is representative part of chimeric alignment, record is as normal; if encompassing chimeric junction, both are recorded as normal</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">bamIrepr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamN</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//the next mate is chimerically split</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bamIrepr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//TODO check flags of SE split read</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if (chimType==3) {</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bamIrepr=bamN;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// } else if (trChim[itr]->exons[0][EX_iFrag]==trChim[1-itr]->exons[0][EX_iFrag]) {</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" 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="LC53" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bamIrepr=( (itr%2)==(trChim[itr]->Str) && chimType!=3) ? bamN+1 : bamN;//this is the mate that is chimerically split</span></span>
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<pre style="margin: 0;">+<span id="LC54" 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;">//"supplementary" chimeric segment</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bamHardClip</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">itr</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="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Str</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">13</span> <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//right:left chimeric junction</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">bamIsuppl</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamN</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimType</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;">//PE alignment, need mate info for the suppl</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex</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="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nExons</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;">iex</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="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Chr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">bamN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">],</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="n" style="color: #333;">RA</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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Chr</span><span class="p">],</span> <span class="n" style="color: #333;">mateChr</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;">mateStart</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">RA</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;">mateChr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RA</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mateChr</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;">mateStrand</span><span class="p">,</span> <span class="n" style="color: #333;">alignType</span><span class="p">,</span> \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">,</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</span><span class="p">,</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</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;">bamBytesTotal</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</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;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//outBAMoneAlignNbytes[1] = 0 if SE is recorded</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//write all bam lines</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">bamN</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 class="c1" style="color: #998; font-style: italic;">//output all pieces</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;">int</span> <span class="n" style="color: #333;">tagI</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">bamIrepr</span><span class="p">)</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;">tagI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamIsuppl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC83" 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;">ii</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">bamIsuppl</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">tagI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamIrepr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="p">};</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tagI</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="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_read1_fromArray</span><span class="p">(</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">tagI</span><span class="p">],</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">auxp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="s" style="color: #d14;">"NM"</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">auxv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_aux2i</span><span class="p">(</span><span class="n" style="color: #333;">auxp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tagSA1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SAZ"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">RA</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;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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;">to_string</span><span class="p">((</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">','</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0x10</span><span class="p">)</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="sc" style="color: #d14;">'+'</span><span class="o" style="font-weight: 600;">:</span><span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bam_cigarString</span><span class="p">(</span><span class="n" style="color: #333;">b</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;">to_string</span><span class="p">((</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="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;">uint</span><span class="p">)</span><span class="n" style="color: #333;">auxv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="sc" style="color: #d14;">';'</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</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;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]),</span> <span class="n" style="color: #333;">tagSA1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">tagSA1</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;">//copy string including \0 at the end</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</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;">tagSA1</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>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// don't use bam_destroy1(), because bam_read1_fromArray does not allocate memory for b->data</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="p">};</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" 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;">outBAMunsorted</span><span class="p">)</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMunsorted</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unsortedOneAlign</span><span class="p">(</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</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="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;">bamBytesTotal</span><span class="p">);</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" 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;">outBAMcoord</span><span class="p">)</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMcoord</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coordOneAlign</span><span class="p">(</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iReadAll</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="p">};</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#40b7d10e4645dc6ae30e5830f3b8abe35c537374"><strong>source/ChimericDetection.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,16 +17,12 @@ class ChimericDetection {</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nWinTr</span><span class="p">;</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <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;">Read1</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outGen</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;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readLength</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">chimN</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ChimericAlign</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chimAligns</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chimRecord</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimScoreBest</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">ChimericDetection</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;">Pin</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">***</span><span class="n" style="color: #333;">trAll</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nWinTr</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;">Read1in</span><span class="p">,</span> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genomeIn</span><span class="p">,</span> <span class="n" style="color: #333;">fstream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ostreamChimJunctionIn</span><span class="p">,</span> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nWin</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readLength<span class="idiff left">In</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxNonChimAlignScore</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">PEmerged_flag</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nWin</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readLength</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxNonChimAlignScore</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ReadAlign</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">PEunmergedRA</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">fstream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ostreamChimJunction</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><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="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include "blocksOverlap.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ChimericDetection.h"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ChimericSegment.h"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ReadAlign.h"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">chimericAlignScore</span> <span class="p">(</span><span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seg1</span><span class="p">,</span> <span class="n" style="color: #333;">ChimericSegment</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seg2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><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">@@ -19,7 +20,7 @@ int chimericAlignScore (ChimericSegment & seg1, ChimericSegment & seg2)</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" 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="LC22" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ChimericDetection</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxNonChimAlignScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">PEmerged_flag</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ChimericDetection</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxNonChimAlignScore</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ReadAlign</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">PEunmergedRA</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// for (uint ii=0;ii<chimAligns.size();ii++) {//deallocate aligns</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if (chimAligns.at(ii).stitchingDone) {//al1,al2 were allocated</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">@@ -36,7 +37,8 @@ bool ChimericDetection::chimericDetectionMult(uint nW, uint *readLength, int max</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">chimScoreBest</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="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimScoreBest</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="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bestChimAlign</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// points to element of chimAligns with highest chimScoreBest</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxPossibleAlignScore</span> <span class="o" style="font-weight: 600;">=</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;">readLength</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;">readLength</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minScoreToConsider</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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">scoreMin</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">@@ -81,10 +83,11 @@ bool ChimericDetection::chimericDetectionMult(uint nW, uint *readLength, int max</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">chimScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chimScoreBest</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;">chimScoreBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">chimScore</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;">bestChimAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chimAligns</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>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chimScoreBest</span> <span class="o" style="font-weight: 600;">-</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;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">multimapScoreRange</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">minScoreToConsider</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// best score increased, so subsequent alignment candidates must score higher</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">minScoreToConsider</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chimScoreBest</span> <span class="o" style="font-weight: 600;">-</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;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">multimapScoreRange</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="LC90" class="line" lang="cpp"> <span class="p">}<span class="idiff left right">;</span></span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// endif stitched chimera survived.</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// al1, al2 allocated during stitching</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,7 +104,7 @@ bool ChimericDetection::chimericDetectionMult(uint nW, uint *readLength, int max</td>
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101
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimScoreBest</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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102
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">chimN</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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">uint</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">chimN</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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105
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108
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<pre style="margin: 0;"> <span id="LC108" 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="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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106
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//scan all chimeras, find the number within score range</span></span>
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107
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minScoreToConsider</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,9 +114,24 @@ bool ChimericDetection::chimericDetectionMult(uint nW, uint *readLength, int max</td>
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111
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimN</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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">multimapNmax</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//too many loci</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"></span>
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114
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<pre style="margin: 0;">-<span id="LC114" 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="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">cAit</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;">//output chimeras within score range</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minScoreToConsider</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">cAit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimericJunctionOutput</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ostreamChimJunction</span><span class="p">,</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">maxNonChimAlignScore</span><span class="p">,</span> <span class="n" style="color: #333;">PEmerged_flag</span><span class="p">,</span> <span class="n" style="color: #333;">chimScoreBest</span><span class="p">,</span> <span class="n" style="color: #333;">maxPossibleAlignScore</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//keep track of "HI" SAM attribute</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</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;">//output chimeras within score range</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chimScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minScoreToConsider</span><span class="p">)</span> <span class="p">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC121" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">junctions</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chimericJunctionOutput</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ostreamChimJunction</span><span class="p">,</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">maxNonChimAlignScore</span><span class="p">,</span> <span class="n" style="color: #333;">PEunmergedRA</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">chimScoreBest</span><span class="p">,</span> <span class="n" style="color: #333;">maxPossibleAlignScore</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="p">{</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// convert merged SE chimera to PE chimera if this is a merged chimera</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PEunmergedRA</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">RA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PEunmergedRA</span><span class="p">;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peOverlapChimericSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al2</span><span class="p">,</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al2</span><span class="p">);</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chimericBAMoutput</span><span class="p">(</span><span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">al2</span><span class="p">,</span> <span class="n" style="color: #333;">chimAligns</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">RA</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bestChimAlign</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">};</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="p">};</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">chimN</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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<li id="6ae9e88712056a2abd55911f4d3a7d8b8145819c">
<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#6ae9e88712056a2abd55911f4d3a7d8b8145819c"><strong>source/Makefile</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">@@ -45,7 +45,7 @@ OBJECTS = soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistri</td>
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45
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"> GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o <span class="se" style="color: #d14;">\</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"> ReadAlign_outputAlignments.o <span class="se" style="color: #d14;">\</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"> ReadAlign.o STAR.o <span class="se" style="color: #d14;">\</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="make"> SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o <span class="se" style="color: #d14;">\</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"> SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o <span class="idiff left right">Parameters_samAttributes.o </span>InOutStreams.o SequenceFuns.o Genome.o Stats.o <span class="se" style="color: #d14;">\</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"> Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o <span class="se" style="color: #d14;">\</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make"> Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="make"> ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(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">@@ -58,8 +58,8 @@ OBJECTS = soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistri</td>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"> ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"> ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o<span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"> ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make"> ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"> stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="make"> ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"> Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"> Genome_insertSequences.o Genome_consensusSequence.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"> insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o <span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#6e7e9199db44be8b0f606c7c21db10763fc8b0eb"><strong>source/Parameters.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">@@ -1003,208 +1003,13 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>
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1003
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1003
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<pre style="margin: 0;"> <span id="LC1003" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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1004
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="cpp"> <span class="p">};</span></span>
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="cpp"> </span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outSAMattributes</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NH</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;">//TODO re-write as class with constructor?</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">HI</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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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">AS</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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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NM</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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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MD</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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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">nM</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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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jM</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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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jI</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1015" 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">
1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</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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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MC</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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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</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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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ch</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="LC1019" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</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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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</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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1022
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</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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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">rB</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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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ha</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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1025
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="cpp"></span>
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1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CR</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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1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CY</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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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UR</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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1029
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UY</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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1030
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CB</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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1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UB</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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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</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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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</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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1034
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sM</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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1035
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sS</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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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sQ</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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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//SAM attributes</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttributes</span><span class="p">();</span></span>
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1037
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> </span>
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1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for quant SAM output only NH and HI flags</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">;</span></span>
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1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="p">.</span><span class="n" style="color: #333;">NH</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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1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="p">.</span><span class="n" style="color: #333;">HI</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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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NH</span><span class="p">);</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_HI</span><span class="p">);</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="cpp"></span>
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1045
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vAttr1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1046" 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">
1046
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1046" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"None"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">-<span id="LC1047" 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;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"All"</span><span class="p">){</span></span>
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1048
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"NH"</span><span class="p">,</span><span class="s" style="color: #d14;">"HI"</span><span class="p">,</span><span class="s" style="color: #d14;">"AS"</span><span class="p">,</span><span class="s" style="color: #d14;">"nM"</span><span class="p">,</span><span class="s" style="color: #d14;">"NM"</span><span class="p">,</span><span class="s" style="color: #d14;">"MD"</span><span class="p">,</span><span class="s" style="color: #d14;">"jM"</span><span class="p">,</span><span class="s" style="color: #d14;">"jI"</span><span class="p">,</span><span class="s" style="color: #d14;">"MC"</span><span class="p">,</span><span class="s" style="color: #d14;">"ch"</span><span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1049" 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">
1049
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<pre style="margin: 0;">-<span id="LC1049" 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;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Standard"</span><span class="p">){</span></span>
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1050
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"NH"</span><span class="p">,</span><span class="s" style="color: #d14;">"HI"</span><span class="p">,</span><span class="s" style="color: #d14;">"AS"</span><span class="p">,</span><span class="s" style="color: #d14;">"nM"</span><span class="p">};</span></span>
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1051
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<pre style="margin: 0;">-<span id="LC1051" 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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1052
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outSAMattributes</span><span class="p">;</span></span>
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1053
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1053" class="line" lang="cpp"> <span class="p">};</span></span>
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1054
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1054" class="line" lang="cpp"></span>
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1055
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1055" 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;">vAttr1</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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<td class="diff-line-num old old_line" data-linenumber="1056" 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">
1056
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1056" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vAttr1</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;">"NH"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1057" 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">
1057
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1057" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NH</span><span class="p">);</span></span>
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1058
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<pre style="margin: 0;">-<span id="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NH</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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1059
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<pre style="margin: 0;">-<span id="LC1059" 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;">vAttr1</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;">"HI"</span><span class="p">)</span> <span class="p">{</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_HI</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1061" 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">
1061
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1061" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">HI</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1062" 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">
1062
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1062" 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;">vAttr1</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;">"AS"</span><span class="p">)</span> <span class="p">{</span></span>
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1063
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1063" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_AS</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1064" 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">
1064
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">AS</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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1065
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1065" 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;">vAttr1</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;">"NM"</span><span class="p">)</span> <span class="p">{</span></span>
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1066
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NM</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1067" 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">
1067
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NM</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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1068
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1068" 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;">vAttr1</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;">"MD"</span><span class="p">)</span> <span class="p">{</span></span>
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1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MD</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1070" 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">
1070
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1070" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MD</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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1071
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1071" 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;">vAttr1</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;">"nM"</span><span class="p">)</span> <span class="p">{</span></span>
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1072
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<pre style="margin: 0;">-<span id="LC1072" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_nM</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1073" 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">
1073
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">nM</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1074" 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">
1074
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1074" 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;">vAttr1</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;">"jM"</span><span class="p">)</span> <span class="p">{</span></span>
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1075
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_jM</span><span class="p">);</span></span>
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1076
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jM</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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1077
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<pre style="margin: 0;">-<span id="LC1077" 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;">vAttr1</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;">"jI"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_jI</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jI</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;">-<span id="LC1080" 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;">vAttr1</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;">"vA"</span><span class="p">)</span> <span class="p">{</span></span>
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1081
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<pre style="margin: 0;">-<span id="LC1081" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vA</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1082" 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">
1082
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1082" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1083" 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">
1083
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1083" 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;">vAttr1</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;">"vG"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;">-<span id="LC1084" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vG</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1085" 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">
1085
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1085" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;">-<span id="LC1086" 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;">vAttr1</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;">"vW"</span><span class="p">)</span> <span class="p">{</span></span>
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1087
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<pre style="margin: 0;">-<span id="LC1087" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1088" 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">
1088
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1088" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1089" 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">
1089
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1089" 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;">vAttr1</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;">"ha"</span><span class="p">)</span> <span class="p">{</span></span>
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1090
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<pre style="margin: 0;">-<span id="LC1090" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ha</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1091" 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">
1091
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1091" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ha</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1092" 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">
1092
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1092" 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;">vAttr1</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;">"RG"</span><span class="p">)</span> <span class="p">{</span></span>
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1093
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1093" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1095" 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">
1095
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</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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1096
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<pre style="margin: 0;">-<span id="LC1096" 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;">vAttr1</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;">"rB"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1097" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_rB</span><span class="p">);</span></span>
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1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_rB</span><span class="p">);</span></span>
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1099
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<pre style="margin: 0;">-<span id="LC1099" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">rB</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1100" 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">
1100
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<pre style="margin: 0;">-<span id="LC1100" 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;">vAttr1</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;">"ch"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1101" 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">
1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ch</span><span class="p">);</span></span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ch</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1103" 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">
1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ch</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1104" 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">
1104
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<pre style="margin: 0;">-<span id="LC1104" 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;">vAttr1</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;">"MC"</span><span class="p">)</span> <span class="p">{</span></span>
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1105
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MC</span><span class="p">);</span></span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MC</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1107" 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">
1107
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MC</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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1108
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<pre style="margin: 0;">-<span id="LC1108" 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;">vAttr1</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;">"CR"</span><span class="p">)</span> <span class="p">{</span></span>
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1109
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CR</span><span class="p">);</span></span>
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1110
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CR</span><span class="p">);</span></span>
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1111
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CR</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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1112
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<pre style="margin: 0;">-<span id="LC1112" 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;">vAttr1</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;">"CY"</span><span class="p">)</span> <span class="p">{</span></span>
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1113
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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CY</span><span class="p">);</span></span>
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1114
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<pre style="margin: 0;">-<span id="LC1114" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CY</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1115" 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">
1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CY</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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1116
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<pre style="margin: 0;">-<span id="LC1116" 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;">vAttr1</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;">"UR"</span><span class="p">)</span> <span class="p">{</span></span>
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1117
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UR</span><span class="p">);</span></span>
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1118
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<pre style="margin: 0;">-<span id="LC1118" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UR</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1119" 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">
1119
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<pre style="margin: 0;">-<span id="LC1119" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UR</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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1120
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<pre style="margin: 0;">-<span id="LC1120" 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;">vAttr1</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;">"UY"</span><span class="p">)</span> <span class="p">{</span></span>
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1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UY</span><span class="p">);</span></span>
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1122
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UY</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1123" 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">
1123
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UY</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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1124
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<pre style="margin: 0;">-<span id="LC1124" 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;">vAttr1</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;">"CB"</span><span class="p">)</span> <span class="p">{</span></span>
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1125
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<pre style="margin: 0;">-<span id="LC1125" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CB</span><span class="p">);</span></span>
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1126
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<pre style="margin: 0;">-<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CB</span><span class="p">);</span></span>
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1127
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<pre style="margin: 0;">-<span id="LC1127" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CB</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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1128
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<pre style="margin: 0;">-<span id="LC1128" 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;">vAttr1</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;">"UB"</span><span class="p">)</span> <span class="p">{</span></span>
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1129
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<pre style="margin: 0;">-<span id="LC1129" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UB</span><span class="p">);</span></span>
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1130
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<pre style="margin: 0;">-<span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UB</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1131" 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">
1131
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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UB</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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1132
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<pre style="margin: 0;">-<span id="LC1132" 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;">vAttr1</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;">"GX"</span><span class="p">)</span> <span class="p">{</span></span>
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1133
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<pre style="margin: 0;">-<span id="LC1133" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GX</span><span class="p">);</span></span>
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1134
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<pre style="margin: 0;">-<span id="LC1134" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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="1135" 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">
1135
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</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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1136
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<pre style="margin: 0;">-<span id="LC1136" 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;">vAttr1</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;">"GN"</span><span class="p">)</span> <span class="p">{</span></span>
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1137
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GN</span><span class="p">);</span></span>
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1138
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GN</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1139" 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">
1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</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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1140
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<pre style="margin: 0;">-<span id="LC1140" 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;">vAttr1</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;">"sM"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1141" 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">
1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sM</span><span class="p">);</span></span>
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1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sM</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1143" 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">
1143
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1143" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sM</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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1144
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<pre style="margin: 0;">-<span id="LC1144" 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;">vAttr1</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;">"sS"</span><span class="p">)</span> <span class="p">{</span></span>
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1145
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sS</span><span class="p">);</span></span>
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1146
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sS</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1147" 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">
1147
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1147" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sS</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="1148" 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">
1148
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<pre style="margin: 0;">-<span id="LC1148" 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;">vAttr1</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;">"sQ"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1149" 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">
1149
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<pre style="margin: 0;">-<span id="LC1149" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sQ</span><span class="p">);</span></span>
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1150
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<pre style="margin: 0;">-<span id="LC1150" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sQ</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1151" 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">
1151
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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sQ</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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1152
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1152" 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;">vAttr1</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;">"XS"</span><span class="p">)</span> <span class="p">{</span></span>
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1153
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<pre style="margin: 0;">-<span id="LC1153" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_XS</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1154" 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">
1154
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1154" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</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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1155
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<pre style="margin: 0;">-<span id="LC1155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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>
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<td class="diff-line-num old old_line" data-linenumber="1156" 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">
1156
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1156" 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;">"WARNING --outSAMattributes contains XS, therefore STAR will use --outSAMstrandField intronMotif"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1157
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1157" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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 old old_line" data-linenumber="1158" 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">
1158
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1158" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1159" 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">
1159
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1159" 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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<td class="diff-line-num old old_line" data-linenumber="1160" 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">
1160
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1160" 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 old old_line" data-linenumber="1161" 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">
1161
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1161" 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;">"EXITING because of FATAL INPUT ERROR: unknown/unimplemented SAM atrribute (tag): "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">vAttr1</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;">"</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 old old_line" data-linenumber="1162" 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">
1162
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1162" 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 STAR with --outSAMattributes that contains only implemented attributes</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 old old_line" data-linenumber="1163" 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">
1163
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1163" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1164" 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">
1164
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1164" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1165" 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">
1165
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1165" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1166" 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">
1166
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1166" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1167" 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">
1167
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1167" 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;">var</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1168" 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">
1168
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1168" 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 old old_line" data-linenumber="1169" 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">
1169
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1169" 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;">"EXITING because of fatal PARAMETER error: --outSAMattributes contains vA and/or vG tag(s), but --varVCFfile is not set</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 old old_line" data-linenumber="1170" 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">
1170
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1170" 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 STAR with a --varVCFfile option, or without vA/vG tags in --outSAMattributes</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 old old_line" data-linenumber="1171" 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">
1171
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1171" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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1172
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1172" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1173" 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">
1173
</td>
<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1173" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1174" 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">
1174
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1174" 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;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1175" 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">
1175
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<pre style="margin: 0;">-<span id="LC1175" 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 old old_line" data-linenumber="1176" 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">
1176
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1176" 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;">"EXITING because of fatal PARAMETER error: --outSAMattributes contains vW tag, but --waspOutputMode is not set</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 old old_line" data-linenumber="1177" 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">
1177
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1177" 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 STAR with a --waspOutputMode option, or without vW tags in --outSAMattributes</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 old old_line" data-linenumber="1178" 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">
1178
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1178" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1179" 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">
1179
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1179" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1180" 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">
1180
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1180" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1181" 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">
1181
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattrRGline</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="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1182" 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">
1182
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1182" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1183" 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">
1183
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1183" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1184" 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">
1184
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1184" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1185" 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">
1185
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1185" 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;">"WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1186" 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">
1186
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1186" 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;">outSAMattrRG</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1187" 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">
1187
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1187" 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 old old_line" data-linenumber="1188" 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">
1188
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1188" 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;">"EXITING because of FATAL INPUT ERROR: --outSAMattributes contains RG tag, but --outSAMattrRGline is not set</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 old old_line" data-linenumber="1189" 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">
1189
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1189" 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 STAR with a valid read group parameter --outSAMattrRGline</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 old old_line" data-linenumber="1190" 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">
1190
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1190" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1191" 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">
1191
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1191" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1192" 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">
1192
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1192" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1193" 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">
1193
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<td class="diff-line-num new_line old" data-linenumber="1009" 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="LC1193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1194" 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">
1194
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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_XS</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1195" 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;">"WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="cpp"> <span class="p">};</span></span>
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1197
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="cpp"></span>
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1198
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<pre style="margin: 0;">-<span id="LC1198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="p">)</span> <span class="p">{</span></span>
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1199
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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1200
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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1201
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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</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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1202
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<pre style="margin: 0;">-<span id="LC1202" 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;">"WARNING --waspOutputMode is set, therefore STAR will output vW attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1203
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<pre style="margin: 0;">-<span id="LC1203" class="line" lang="cpp"> <span class="p">};</span></span>
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1204
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<pre style="margin: 0;">-<span id="LC1204" class="line" lang="cpp"></span>
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1205
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//solo</span></span>
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1206
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">initialize</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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1207
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//alignEnds</span></span>
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1208
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">alignEndsType</span><span class="p">.</span><span class="n" style="color: #333;">ext</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1209
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<td class="diff-line-num new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">alignEndsType</span><span class="p">.</span><span class="n" style="color: #333;">ext</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1210
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp"> <span class="n" style="color: #333;">alignEndsType</span><span class="p">.</span><span class="n" style="color: #333;">ext</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1392" style="width: 35px; color: rgba(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="1197" style="width: 35px; color: rgba(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">@@ -1392,8 +1197,6 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>
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1392
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1197
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<pre style="margin: 0;"> <span id="LC1197" 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;">"Finished loading and checking parameters</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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1393
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="cpp"><span class="p">};</span></span>
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1394
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1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="cpp"></span>
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1395
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<pre style="margin: 0;"> <span id="LC1200" 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="LC1201" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Parameters</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">scanAllLines</span> <span class="p">(</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">streamIn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inputLevel</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inputLevelRequested</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//scan</span></span>
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// istringstream stringInStream (stringIn);</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">@@ -1468,6 +1271,3 @@ int Parameters::scanOneLine (string &lineIn, int inputLevel, int inputLevelReque</td>
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="cpp"><span class="p">};</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#09b38547a28087b813616bd2a7334493c3862c48"><strong>source/Parameters.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -348,6 +348,7 @@ class Parameters {</td>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">readFilesInit</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">closeReadsFiles</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">readSAMheader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">readFilesCommandString</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readFilesNames</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">samAttributes</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">attrYes</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">attrTag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // Parameters.h</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#f09ea75b8243d42eee54c10d49465997ac00609f"><strong>source/ParametersChimeric_initialize.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">@@ -80,10 +80,10 @@ void ParametersChimeric::initialize(Parameters *pPin)</td>
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<pre style="margin: 0;"> <span id="LC80" 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="LC81" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">multimapNmax</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="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">out</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bam</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">out</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">samOld</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">multimapNmax</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;"><span class="idiff left">out</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">samOld</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC84" 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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<pre style="margin: 0;">-<span id="LC85" 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;">"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions</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="LC86" 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 with --chimOutType Junctions</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;">errOut</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions<span class="idiff left right">/WithinBAM</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" 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 with --chimOutType Junctions<span class="idiff left right">/WithinBAM</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC87" 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="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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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#cede17459d086a5e7ad5b0dbcfff22b4e4861435"><strong>source/Parameters_samAttributes.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Parameters.h"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ErrorWarning.h"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Parameters</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">samAttributes</span><span class="p">(){</span><span class="c1" style="color: #998; font-style: italic;">//everything related to SAM attributes</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outSAMattributes</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NH</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;">//TODO re-write as class with constructor?</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">HI</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="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">AS</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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NM</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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MD</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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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">nM</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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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jM</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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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jI</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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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MC</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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ch</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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">rB</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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ha</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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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CR</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CY</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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UR</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UY</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="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CB</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UB</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="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</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="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</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="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sM</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="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sS</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="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sQ</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="LC36" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for quant SAM output only NH and HI flags</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="p">.</span><span class="n" style="color: #333;">NH</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="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresentQuant</span><span class="p">.</span><span class="n" style="color: #333;">HI</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="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NH</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_HI</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vAttr1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"None"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"All"</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"NH"</span><span class="p">,</span><span class="s" style="color: #d14;">"HI"</span><span class="p">,</span><span class="s" style="color: #d14;">"AS"</span><span class="p">,</span><span class="s" style="color: #d14;">"nM"</span><span class="p">,</span><span class="s" style="color: #d14;">"NM"</span><span class="p">,</span><span class="s" style="color: #d14;">"MD"</span><span class="p">,</span><span class="s" style="color: #d14;">"jM"</span><span class="p">,</span><span class="s" style="color: #d14;">"jI"</span><span class="p">,</span><span class="s" style="color: #d14;">"MC"</span><span class="p">,</span><span class="s" style="color: #d14;">"ch"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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;">outSAMattributes</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="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Standard"</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"NH"</span><span class="p">,</span><span class="s" style="color: #d14;">"HI"</span><span class="p">,</span><span class="s" style="color: #d14;">"AS"</span><span class="p">,</span><span class="s" style="color: #d14;">"nM"</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC50" 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="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">vAttr1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outSAMattributes</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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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" 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;">vAttr1</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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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vAttr1</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;">"NH"</span><span class="p">)</span> <span class="p">{</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NH</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NH</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 new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" 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;">vAttr1</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;">"HI"</span><span class="p">)</span> <span class="p">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_HI</span><span class="p">);</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">HI</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 new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="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;">vAttr1</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;">"AS"</span><span class="p">)</span> <span class="p">{</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_AS</span><span class="p">);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">AS</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 new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" 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;">vAttr1</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;">"NM"</span><span class="p">)</span> <span class="p">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_NM</span><span class="p">);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NM</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 new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" 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;">vAttr1</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;">"MD"</span><span class="p">)</span> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MD</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MD</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="LC70" 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;">vAttr1</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;">"nM"</span><span class="p">)</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_nM</span><span class="p">);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">nM</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 new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" 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;">vAttr1</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;">"jM"</span><span class="p">)</span> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_jM</span><span class="p">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jM</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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76
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<pre style="margin: 0;">+<span id="LC76" 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;">vAttr1</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;">"jI"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_jI</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">jI</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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79
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<pre style="margin: 0;">+<span id="LC79" 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;">vAttr1</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;">"vA"</span><span class="p">)</span> <span class="p">{</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vA</span><span class="p">);</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</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 new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="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;">vAttr1</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;">"vG"</span><span class="p">)</span> <span class="p">{</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vG</span><span class="p">);</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="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;">vAttr1</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;">"vW"</span><span class="p">)</span> <span class="p">{</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</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="LC88" 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;">vAttr1</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;">"ha"</span><span class="p">)</span> <span class="p">{</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ha</span><span class="p">);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ha</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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91
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<pre style="margin: 0;">+<span id="LC91" 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;">vAttr1</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;">"RG"</span><span class="p">)</span> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</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="LC95" 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;">vAttr1</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;">"rB"</span><span class="p">)</span> <span class="p">{</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_rB</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_rB</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">rB</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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99
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<pre style="margin: 0;">+<span id="LC99" 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;">vAttr1</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;">"ch"</span><span class="p">)</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ch</span><span class="p">);</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_ch</span><span class="p">);</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ch</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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103
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<pre style="margin: 0;">+<span id="LC103" 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;">vAttr1</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;">"MC"</span><span class="p">)</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MC</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_MC</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">MC</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="LC107" 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;">vAttr1</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;">"CR"</span><span class="p">)</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CR</span><span class="p">);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CR</span><span class="p">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CR</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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111
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<pre style="margin: 0;">+<span id="LC111" 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;">vAttr1</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;">"CY"</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CY</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CY</span><span class="p">);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CY</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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115
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<pre style="margin: 0;">+<span id="LC115" 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;">vAttr1</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;">"UR"</span><span class="p">)</span> <span class="p">{</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UR</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UR</span><span class="p">);</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UR</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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119
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<pre style="margin: 0;">+<span id="LC119" 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;">vAttr1</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;">"UY"</span><span class="p">)</span> <span class="p">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UY</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UY</span><span class="p">);</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UY</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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123
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<pre style="margin: 0;">+<span id="LC123" 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;">vAttr1</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;">"CB"</span><span class="p">)</span> <span class="p">{</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CB</span><span class="p">);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_CB</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CB</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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127
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<pre style="margin: 0;">+<span id="LC127" 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;">vAttr1</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;">"UB"</span><span class="p">)</span> <span class="p">{</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UB</span><span class="p">);</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_UB</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UB</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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131
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<pre style="margin: 0;">+<span id="LC131" 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;">vAttr1</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;">"GX"</span><span class="p">)</span> <span class="p">{</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GX</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GX</span><span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</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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135
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<pre style="margin: 0;">+<span id="LC135" 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;">vAttr1</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;">"GN"</span><span class="p">)</span> <span class="p">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GN</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_GN</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</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 new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="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;">vAttr1</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;">"sM"</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sM</span><span class="p">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sM</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sM</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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143
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<pre style="margin: 0;">+<span id="LC143" 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;">vAttr1</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;">"sS"</span><span class="p">)</span> <span class="p">{</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sS</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sS</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sS</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 new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="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;">vAttr1</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;">"sQ"</span><span class="p">)</span> <span class="p">{</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sQ</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_sQ</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sQ</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 new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="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;">vAttr1</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;">"XS"</span><span class="p">)</span> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_XS</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</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 new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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>
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155
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<pre style="margin: 0;">+<span id="LC155" 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;">"WARNING --outSAMattributes contains XS, therefore STAR will use --outSAMstrandField intronMotif"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="p">};</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" 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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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="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 new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <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 INPUT ERROR: unknown/unimplemented SAM atrribute (tag): "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">vAttr1</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;">"</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 new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="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 STAR with --outSAMattributes that contains only implemented attributes</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 new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="p">};</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="p">};</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC166" 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;">var</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</span><span class="p">))</span> <span class="p">{</span></span>
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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">
167
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<pre style="margin: 0;">+<span id="LC167" 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 new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" 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;">"EXITING because of fatal PARAMETER error: --outSAMattributes contains vA and/or vG tag(s), but --varVCFfile is not set</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 new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" 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 STAR with a --varVCFfile option, or without vA/vG tags in --outSAMattributes</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 new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="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;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="p">)</span> <span class="p">{</span></span>
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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="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 new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" 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;">"EXITING because of fatal PARAMETER error: --outSAMattributes contains vW tag, but --waspOutputMode is not set</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 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="n" style="color: #333;">errOut</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"SOLUTION: re-run STAR with a --waspOutputMode option, or without vW tags in --outSAMattributes</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 new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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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="p">};</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattrRGline</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="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_RG</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</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 new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="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;">"WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" 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;">outSAMattrRG</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span> <span class="p">{</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" 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 new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <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 INPUT ERROR: --outSAMattributes contains RG tag, but --outSAMattrRGline is not set</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 new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="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 STAR with a valid read group parameter --outSAMattrRGline</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 new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="p">};</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMstrandField</span><span class="p">.</span><span class="n" style="color: #333;">type</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">XS</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_XS</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="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;">"WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="p">};</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrOrderQuant</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ATTR_vW</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</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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201
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<pre style="margin: 0;">+<span id="LC201" 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;">"WARNING --waspOutputMode is set, therefore STAR will output vW attribute"</span> <span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="p">};</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TODO: BAM-only flag should all have values > 100</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">ch</span><span class="p">,</span> <span class="s" style="color: #d14;">"ch"</span><span class="p">);</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CR</span><span class="p">,</span> <span class="s" style="color: #d14;">"CR"</span><span class="p">);</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CY</span><span class="p">,</span> <span class="s" style="color: #d14;">"CY"</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UR</span><span class="p">,</span> <span class="s" style="color: #d14;">"UR"</span><span class="p">);</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UY</span><span class="p">,</span> <span class="s" style="color: #d14;">"UY"</span><span class="p">);</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">CB</span><span class="p">,</span> <span class="s" style="color: #d14;">"CB"</span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">UB</span><span class="p">,</span> <span class="s" style="color: #d14;">"UB"</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sM</span><span class="p">,</span> <span class="s" style="color: #d14;">"sM"</span><span class="p">);</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sS</span><span class="p">,</span> <span class="s" style="color: #d14;">"sS"</span><span class="p">);</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">sQ</span><span class="p">,</span> <span class="s" style="color: #d14;">"sQ"</span><span class="p">);</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">rB</span><span class="p">,</span> <span class="s" style="color: #d14;">"rB"</span><span class="p">);</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vG</span><span class="p">,</span> <span class="s" style="color: #d14;">"vG"</span><span class="p">);</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vA</span><span class="p">,</span> <span class="s" style="color: #d14;">"vA"</span><span class="p">);</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">vW</span><span class="p">,</span> <span class="s" style="color: #d14;">"vW"</span><span class="p">);</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</span><span class="p">,</span> <span class="s" style="color: #d14;">"GX"</span><span class="p">);</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</span><span class="p">,</span> <span class="s" style="color: #d14;">"GN"</span><span class="p">);</span> </span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GX</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">GN</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//turn on quantification </span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <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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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <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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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Parameters</span><span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">samAttrRequiresBAM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">attrYes</span><span class="p">,</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">attrTag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC229" 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;">attrYes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// nothing to do</span></span>
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<pre style="margin: 0;">+<span id="LC231" 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;">outBAMunsorted</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outBAMcoord</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC232" 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 new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <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 PARAMETER error: --outSAMattributes contains "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">attrTag</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" tag, which requires BAM output.</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="LC234" 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 STAR with --outSAMtype BAM Unsorted (and/or) SortedByCoordinate option, or without "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">attrTag</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" tag in --outSAMattributes</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="LC235" 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;">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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outSAMbool</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC239" 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;">"WARNING: --outSAMattributes contains "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">attrTag</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" tag. It will be output into BAM file(s), but not SAM 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="LC240" class="line" lang="cpp"><span class="p">};</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#238ae46f3e2ae6c05a1eca3f159a54222230394e"><strong>source/ReadAlign.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,11 +62,17 @@ class ReadAlign {</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peMergeRA</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//ReadAlign for merged PE mates</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">ChimericDetection</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chimDet</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">peOverlapChimericSEtoPE</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn2</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut1</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">SoloRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">soloRead</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//counts reads per CB per and outputs CB/UMI/gene into file, per thread</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">SpliceGraph</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">splGraph</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//input,output</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <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;">outBAMoneAlign</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;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">trChrStart</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unmapType</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mateMapped</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">outSAMattrOrder</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;">outBAMarray</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outBAMarrayN</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <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="c1" style="color: #998; font-style: italic;">//pointer to the parameters, will be initialized on construction</span></span>
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<pre style="margin: 0;"> <span id="LC78" 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">@@ -82,9 +88,6 @@ class ReadAlign {</td>
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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;">//input,output</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <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;">outBAMoneAlign</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;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">samStreamCIGAR</span><span class="p">,</span> <span class="n" style="color: #333;">samStreamSJmotif</span><span class="p">,</span> <span class="n" style="color: #333;">samStreamSJintron</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">matesCIGAR</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC93" 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">@@ -165,10 +168,11 @@ class ReadAlign {</td>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">storeAligns</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iDir</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">Shift</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">Nrep</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">L</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">indStartEnd</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iFrag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">outputTranscript</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outBED</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">outputTranscriptSAM</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unmapType</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mateMapped</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;">outStream</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">outputSpliceGraphSAM</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTrOut</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;">outStream</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">trChrStart</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unmapType</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mateMapped</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">outSAMattrOrder</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;">outBAMarray</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outBAMarrayN</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">samAttrNM_MD</span> <span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">iEx1</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iEx2</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tagNM</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;">tagMD</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">outputTranscriptSJ</span><span class="p">(</span><span class="n" style="color: #333;">Transcript</span> <span class="k" style="font-weight: 600;">const</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;">uint</span> <span class="n" style="color: #333;">nTrOut</span><span class="p">,</span> <span class="n" style="color: #333;">OutSJ</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outStream</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">sjReadStartN</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#0f351bd6f52ff0c9ab03a4771ab917025e709afc"><strong>source/ReadAlignChunk.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">@@ -77,13 +77,15 @@ ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkFstreamOpen</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFileTmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Chimeric.out.junction.thread"</span><span class="p">,</span> <span class="n" style="color: #333;">iChunk</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutChimJunction</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" 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;">outReadsUnmapped</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Fastx"</span> <span class="p">)</span> <span class="p">{</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">chunkFstreamOpen</span></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">outFileTmp</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">"/Unmapped.out.mate1.thread"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">iChunk</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RA</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">chunkOutUnmappedReadsStream</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]);</span></span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" 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">readNmatesIn</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chunkFstreamOpen</span></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">outFileTmp</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">"/Unmapped.out.mate2.thread"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">iChunk</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RA</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">chunkOutUnmappedReadsStream</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">uint32</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">imate</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">readNmatesIn</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">imate</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">chunkFstreamOpen</span></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">outFileTmp</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">"/Unmapped.out.mate"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">to_string</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="s" style="color: #d14;"><span class="idiff">".thread"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">iChunk</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RA</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">chunkOutUnmappedReadsStream</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">imate</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"></span>
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84
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86
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<pre style="margin: 0;"> <span id="LC86" 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;">outFilterType</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"BySJout"</span><span class="p">)</span> <span class="p">{</span></span>
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85
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkFstreamOpen</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFileTmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/FilterBySJoutFiles.mate1.thread"</span><span class="p">,</span><span class="n" style="color: #333;">iChunk</span><span class="p">,</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutFilterBySJoutFiles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" 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;">readNmates</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">chunkFstreamOpen</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFileTmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/FilterBySJoutFiles.mate2.thread"</span><span class="p">,</span><span class="n" style="color: #333;">iChunk</span><span class="p">,</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutFilterBySJoutFiles</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="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;">readNmates</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">chunkFstreamOpen</span><span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outFileTmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/FilterBySJoutFiles.mate2.thread"</span><span class="p">,</span><span class="n" style="color: #333;">iChunk</span><span class="p">,</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutFilterBySJoutFiles</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//here we do not output barcode read</span></span></span>
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87
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;"> <span id="LC91" 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;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</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">@@ -94,6 +96,8 @@ ReadAlignChunk::ReadAlignChunk(Parameters& Pin, Genome &genomeIn, Transcriptome</td>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutChimJunction</span><span class="p">;</span></span>
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95
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutChimJunction</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutChimJunction</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//point to the same out-stream</span></span>
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96
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimDet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ostreamChimJunction</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chunkOutChimJunction</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMunsorted</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMunsorted</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMcoord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">RA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outBAMcoord</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="p">};</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#764c3cfc36fad2f293fd356112b8836ea61e0b02"><strong>source/ReadAlign_alignBAM.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">@@ -184,11 +184,8 @@ int ReadAlign::alignBAM(Transcript const &trOut, uint nTrOut, uint iTrOut, uint</td>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readFilter</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'Y'</span><span class="p">)</span> <span class="n" style="color: #333;">samFLAG</span><span class="o" style="font-weight: 600;">|=</span><span class="mh" style="color: #099;">0x200</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//not passing quality control</span></span>
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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">13</span><span class="p">)</span> <span class="p">{</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">samFLAG</span><span class="o" style="font-weight: 600;">|=</span><span class="mh" style="color: #099;">0x800</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//mark chimeric alignments</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" 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;">//only non-chimeric alignments will be marked as non-primary, since chimeric are already marked with 0x800</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" 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;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">primaryFlag</span><span class="p">)</span> <span class="n" style="color: #333;">samFLAG</span><span class="o" style="font-weight: 600;">|=</span><span class="mh" style="color: #099;">0x100</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//mark not primary align</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">13</span><span class="p">)</span> <span class="n" style="color: #333;">samFLAG</span><span class="o" style="font-weight: 600;">|=</span><span class="mh" style="color: #099;">0x800</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//mark chimeric alignments</span></span>
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<pre style="margin: 0;">+<span id="LC188" 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;">trOut</span><span class="p">.</span><span class="n" style="color: #333;">primaryFlag</span><span class="p">)</span> <span class="n" style="color: #333;">samFLAG</span><span class="o" style="font-weight: 600;">|=</span><span class="mh" style="color: #099;">0x100</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//mark not primary align</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">iEx1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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="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;">iExMate</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="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">iEx2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">iExMate</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;">nExons</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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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#af060c7d950c0018c9102e5f40dcb6ce74317aa8"><strong>source/ReadAlign_chimericDetection.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">@@ -46,7 +46,7 @@ void ReadAlign::chimericDetection() {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimericDetectionOld</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">chimericDetectionOldOutput</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC48" 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;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">readLength</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;">readLength</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">nonchimScoreDropMin</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//require big enough drop in the best score</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimDet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">false</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chimDet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">NULL</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">chimRecord</span> <span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#e567212bd90532effae5cceb340251e161d1e96e"><strong>source/ReadAlign_chimericDetectionOldOutput.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ReadAlign.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BAMfunctions.h"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ChimericAlign.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReadAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericDetectionOldOutput</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" 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">@@ -7,110 +8,31 @@ void ReadAlign::chimericDetectionOldOutput() {</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">chimN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//this is hard-coded for now</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//re-calculate the score for chimeric transcripts</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">alignScore</span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">,</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">G</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="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">alignScore</span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">,</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">G</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="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimRepresent</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">999</span><span class="p">,</span> <span class="n" style="color: #333;">chimType</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="LC16" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 has both mates</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</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="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</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="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//paired portion is primary</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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="LC21" 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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr1 has both mates</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</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="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</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="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//paired portion is primary</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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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26
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<pre style="margin: 0;">-<span id="LC26" 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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 and tr1 are single different mates</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</span> <span class="o" style="font-weight: 600;">=</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;">chimType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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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31
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<pre style="margin: 0;">-<span id="LC31" 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;">//two chimeric segments are on the same mate - this can only happen for single-end reads</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRepresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">maxScore</span><span class="p">)</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>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">chimType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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="LC36" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"></span>
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38
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<pre style="margin: 0;">-<span id="LC38" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//BAM output</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignType</span><span class="p">,</span> <span class="n" style="color: #333;">bamN</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;">bamIsuppl</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;">bamIrepr</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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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">bamBytesTotal</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//estimate of the total size of all bam records, for output buffering</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span><span class="n" style="color: #333;">mateStart</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">itr</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;">itr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimN</span><span class="p">;</span><span class="n" style="color: #333;">itr</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;">//generate bam for all chimeric pieces</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimType</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;">//PE, encompassing</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" 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;">//spanning chimeric alignment, could be PE or SE</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">mateChr</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;">mateStart</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;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//no need fot mate info unless this is the supplementary alignment</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimRepresent</span><span class="o" style="font-weight: 600;">==</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;">itr</span><span class="p">)</span> <span class="p">{</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">10</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//this is representative part of chimeric alignment, record is as normal; if encompassing chimeric junction, both are recorded as normal</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">bamIrepr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamN</span><span class="p">;</span></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="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//the next mate is chimerically split</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bamIrepr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// if (chimType==3) {</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bamIrepr=bamN;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// } else if (trChim[itr].exons[0][EX_iFrag]==trChim[1-itr].exons[0][EX_iFrag]) {</span></span>
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<pre style="margin: 0;">-<span id="LC60" 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="LC61" 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="LC62" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bamIrepr=( (itr%2)==(trChim[itr].Str) && chimType!=3) ? bamN+1 : bamN;//this is the mate that is chimerically split</span></span>
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<pre style="margin: 0;">-<span id="LC63" 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;">//"supplementary" chimeric segment</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">alignType</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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bamHardClip</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">itr</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="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Str</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">13</span> <span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//right:left chimeric junction</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">bamIsuppl</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamN</span><span class="p">;</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chimType</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;">//PE alignment, need mate info for the suppl</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex</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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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">nExons</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;">iex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="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="LC71" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <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;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="p">};</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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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="p">};</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//BAM output</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">ChimericAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericBAMoutput</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trChim</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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">);</span></span>
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80
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">bamN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span 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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">],</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">mateStart</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;">mateChr</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mateChr</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;">mateStrand</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;">alignType</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">,</span> <span class="n" style="color: #333;">outBAMoneAlign</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</span><span class="p">,</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</span><span class="p">);</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">bamBytesTotal</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">outBAMoneAlignNbytes</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;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//outBAMoneAlignNbytes[1] = 0 if SE is recorded</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="p">};</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//write all bam lines</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">bamN</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 class="c1" style="color: #998; font-style: italic;">//output all pieces</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tagI</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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89
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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;">ii</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">bamIrepr</span><span class="p">)</span> <span class="p">{</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">tagI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamIsuppl</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" 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;">ii</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">bamIsuppl</span><span class="p">)</span> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">tagI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bamIrepr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="p">};</span></span>
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94
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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;">tagI</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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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_read1_fromArray</span><span class="p">(</span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">tagI</span><span class="p">],</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">auxp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="s" style="color: #d14;">"NM"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">auxv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bam_aux2i</span><span class="p">(</span><span class="n" style="color: #333;">auxp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tagSA1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SAZ"</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;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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;">to_string</span><span class="p">((</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">','</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0x10</span><span class="p">)</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="sc" style="color: #d14;">'+'</span><span class="o" style="font-weight: 600;">:</span><span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bam_cigarString</span><span class="p">(</span><span class="n" style="color: #333;">b</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;">to_string</span><span class="p">((</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="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;">uint</span><span class="p">)</span><span class="n" style="color: #333;">auxv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="sc" style="color: #d14;">';'</span> <span class="p">;</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">outBAMoneAlign</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;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]),</span> <span class="n" style="color: #333;">tagSA1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">tagSA1</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;">//copy string including \0 at the end</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">outBAMoneAlignNbytes</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;">tagSA1</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>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="p">};</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">samOld</span><span class="p">)</span> <span class="p">{</span></span>
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107
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
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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;">outBAMunsorted</span><span class="p">)</span> <span class="n" style="color: #333;">outBAMunsorted</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unsortedOneAlign</span><span class="p">(</span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</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="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;">bamBytesTotal</span><span class="p">);</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="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;">outBAMcoord</span><span class="p">)</span> <span class="n" style="color: #333;">outBAMcoord</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">coordOneAlign</span><span class="p">(</span><span class="n" style="color: #333;">outBAMoneAlign</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333;">iReadAll</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">);</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">chimN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//this is hard-coded for now</span></span>
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21
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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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 has both mates</span></span>
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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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//paired portion is primary</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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="LC24" 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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</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;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr1 has both mates</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//paired portion is primary</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//tr0 and tr1 are single different mates</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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 new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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 new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="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;">//two chimeric segments are on the same mate - this can only happen for single-end reads</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chimRepresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">maxScore</span><span class="p">)</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>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">chimRepresent</span><span class="p">].</span><span class="n" style="color: #333;">primaryFlag</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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110
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="p">};</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="p">};</span></span>
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112
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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113
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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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">samOld</span><span class="p">)</span> <span class="p">{</span></span>
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114
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36
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<pre style="margin: 0;"> <span id="LC36" 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;">iTr</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;">iTr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimN</span><span class="p">;</span><span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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115
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//write all chimeric pieces to Chimeric.out.sam/junction</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">
116
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38
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<pre style="margin: 0;"> <span id="LC38" 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;">readNmates</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;">//PE: need mate info</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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">@@ -149,4 +71,4 @@ void ReadAlign::chimericDetectionOldOutput() {</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <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;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"><span class="p">};</span></span></pre>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="p">};</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#32c87d85b8e6a7f392241db417a7cd034f3e79d7"><strong>source/ReadAlign_chimericDetectionPEmerged.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ReadAlign.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BAMfunctions.h"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReadAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">chimericDetectionPEmerged</span><span class="p">(</span><span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seRA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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>
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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">@@ -20,59 +21,14 @@ void ReadAlign::chimericDetectionPEmerged(ReadAlign &seRA) {</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//convert merged into PE</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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="mi" style="color: #099;">2</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="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</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;">trInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">mateStart</span><span class="p">,</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <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="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">//segment length [trChim][mate]</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//last exon of the mate0 [trChim]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segLmin</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1LLU</span><span class="p">,</span> <span class="n" style="color: #333;">i1</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;">i2</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="LC32" 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="mi" style="color: #099;">2</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="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" 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;">iex</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;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span> <span class="n" style="color: #333;">iex</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="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">segEx</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;">iex</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">jj</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;">jj</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">jj</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="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">segLmin</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">segLmin</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">segLmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ii</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//trChim of the shortest segment length</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jj</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//mate of the shortest segment length</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i2</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;">//eliminate mate1: simply cut the exons that belong to mate1</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" 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;">//eliminate mate 0: shift mate1 exon to the beginning</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" 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;">iex</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;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span> <span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" 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;">EX_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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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">];</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="p">};</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</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;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</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="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">peOverlapChimericSEtoPE</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trChim</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;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trChim</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="n" style="color: #333;">trChim</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;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">chimericDetectionOldOutput</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC27" 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;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">readLength</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;">readLength</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">nonchimScoreDropMin</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//require big enough drop in the best score</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="c1" style="color: #998; font-style: italic;">// new chimeric detection routine</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">chimDet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">t<span class="idiff left right">rue</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">chimRecord</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">chimDet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chimericDetectionMult</span><span class="p">(</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nW</span><span class="p">,</span> <span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">readLength</span><span class="p">,</span> <span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">t<span class="idiff left right">his</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">chimRecord</span> <span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#38255560373004439a41922897da553297a784d2"><strong>source/ReadAlign_outputAlignments.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="250" style="width: 35px; color: rgba(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="250" style="width: 35px; color: rgba(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">@@ -250,11 +250,10 @@ void ReadAlign::outputAlignments() {</td>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</span><span class="p">[</span><span class="n" style="color: #333;">im</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">Qual0</span><span class="p">[</span><span class="n" style="color: #333;">im</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="LC251" class="line" lang="cpp"> <span class="p">};</span></span>
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="p">};</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" 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;">type</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;">//need to output 2nd (barcode) read</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</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="n" style="color: #333;">readNameMates</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="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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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">qualStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readNameExtra</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</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="n" style="color: #333;">readNameExtra</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">qualStart</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</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="n" style="color: #333;">readNameExtra</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">qualStart</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;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" 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;">readNmatesIn</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="p">{</span><span class="c1" style="color: #998; font-style: italic;">//need to output 2nd (barcode) read, FASTQ only</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmatesIn</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;">readNameMates</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="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="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmatesIn</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;">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;">bSeq</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">chunkOutUnmappedReadsStream</span><span class="p">[</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmatesIn</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;">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;">bQual</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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258
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="p">};</span></span>
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259
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"><span class="p">};</span></span>
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<li id="d938845d26281b751fbd64471e18f13e3c550aa8">
<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#d938845d26281b751fbd64471e18f13e3c550aa8"><strong>source/ReadAlign_outputTranscriptSAM.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" style="width: 35px; color: rgba(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">@@ -344,6 +344,8 @@ uint ReadAlign::outputTranscriptSAM(Transcript const &trOut, uint nTrOut, uint i</td>
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_vG</span><span class="p">:</span></span>
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345
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_vA</span><span class="p">:</span></span>
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346
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ATTR_vW</span><span class="p">:</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="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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<pre style="margin: 0;">+<span id="LC348" 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>
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347
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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348
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="nl">default:</span></span>
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349
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351
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<pre style="margin: 0;"> <span id="LC351" 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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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#188667251bde9bacea8550ecde93b515b078a8a4"><strong>source/ReadAlign_peOverlapMergeMap.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">@@ -141,7 +141,7 @@ void ReadAlign::peMergeMates() {</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="p">};</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Transcript</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//convert alignment from merged-SE to PE</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Transcript</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//convert alignment from merged-SE to PE</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mLen</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">mLen</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;">readLength</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">Str</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">@@ -222,6 +222,11 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">MAX_N_EXONS</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//cannot transform this alignment to PE, too many exons</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">maxScore</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="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">nExons</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="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</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;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//marks "junction" between mates</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">nExons</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;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,28 +273,97 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReadAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">ReadAlign</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seRA</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//ReAdAlign: convert SE to PE and copy</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">nW</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nW</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">nWinTr</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nWinTr</span><span class="p">,</span> <span class="n" style="color: #333;">nW</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nWinTr</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>nW=seRA.nW;</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>memcpy((void*) nWinTr, (void*) seRA.nWinTr, nW*sizeof(*nWinTr));</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">trNtotal</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="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">intScore</span> <span class="n" style="color: #333;">bestScore</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Lread</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trArray</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//just to initialize - to the 0th spot in the trArray</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" 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;">iW</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;">iW</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nW</span><span class="p">;</span> <span class="n" style="color: #333;">iW</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 windows</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trArrayPointer</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">trNtotal</span><span class="p">;</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="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;">iTr</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;">iTr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nWinTr</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">];</span> <span class="n" style="color: #333;">iTr</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 transcripts</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">trNtotal</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]</span><span class="o" style="font-weight: 600;">=*</span><span class="n" style="color: #333;">trInit</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]);</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignScore</span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">,</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">G</span><span class="p">,</span><span class="n" style="color: #333;">P</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</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;">maxScore</span><span class="p">)</span> <span class="p">{</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">],</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> </span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">iW1</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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284
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<pre style="margin: 0;">+<span id="LC284" 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;">iW</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;">iW</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nW</span><span class="p">;</span> <span class="n" style="color: #333;">iW</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 windows</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trArrayPointer</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">trNtotal</span><span class="p">;</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">iTr1</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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287
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<pre style="margin: 0;">+<span id="LC287" 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;">iTr</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;">iTr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">nWinTr</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">];</span> <span class="n" style="color: #333;">iTr</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 transcripts</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=*</span><span class="n" style="color: #333;">trInit</span><span class="p">;</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seRA</span><span class="p">.</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nExons</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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292
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<pre style="margin: 0;">+<span id="LC292" 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;">//conversion did not work</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> </span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignScore</span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">,</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">G</span><span class="p">,</span><span class="n" style="color: #333;">P</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</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;">maxScore</span><span class="p">)</span> <span class="p">{</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="n" style="color: #333;">iTr1</span><span class="p">],</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="p">};</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> </span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iTr1</span><span class="p">;</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">trNtotal</span><span class="p">;</span> </span>
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287
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="p">};</span></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</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;">maxScore</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="p">{</span></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">bestScore</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">;</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iTr1</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;">//if conversion worked for at least one align</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">nWinTr</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">iTr1</span><span class="p">;</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</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;">maxScore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestScore</span><span class="p">)</span> <span class="p">{</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trAll</span><span class="p">[</span><span class="n" style="color: #333;">iW1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">bestScore</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trBest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">maxScore</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="p">};</span> </span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iW1</span><span class="p">;</span></span>
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291
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="p">};</span></span>
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="p">};</span></span>
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293
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">nW</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">iW1</span><span class="p">;</span></span>
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294
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"><span class="p">};</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReadAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">peOverlapChimericSEtoPE</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn2</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut1</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut2</span><span class="p">)</span> <span class="p">{</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//convert merged into PE</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">Transcript</span> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</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;">trInit</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</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="n" style="color: #333;">trInit</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">mateStart</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn1</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">mateStart</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seTrIn2</span><span class="p">);</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">//segment length [tempTrChim][mate]</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//last exon of the mate0 [tempTrChim]</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">segLmin</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1LLU</span><span class="p">,</span> <span class="n" style="color: #333;">i1</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;">i2</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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328
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<pre style="margin: 0;">+<span id="LC328" 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="mi" style="color: #099;">2</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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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" 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;">iex</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;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span> <span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</span><span class="p">];</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">segEx</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;">iex</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC335" 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="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</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="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="p">};</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="p">};</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" 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;">jj</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;">jj</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">segLmin</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">segLmin</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">segLmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">];</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ii</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//tempTrChim of the shortest segment length</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jj</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//mate of the shortest segment length</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="p">};</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="p">};</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i2</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;">//eliminate mate1: simply cut the exons that belong to mate1</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" 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;">//eliminate mate 0: shift mate1 exon to the beginning</span></span>
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<pre style="margin: 0;">+<span id="LC351" 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;">iex</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;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span> <span class="n" style="color: #333;">iex</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="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC353" 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;">EX_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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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</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;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="n" style="color: #333;">ii</span><span class="p">];</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="p">};</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">];</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</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;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</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="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="p">};</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">segEx</span><span class="p">[</span><span class="n" style="color: #333;">i1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">peTrOut2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tempTrChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#2ce04271e5214fcd449bb4917e94be04695c6534"><strong>source/SoloFeature_cellFiltering.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">@@ -21,7 +21,7 @@ void SoloFeature::cellFiltering()</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">nUMImax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nUMIperCBsorted</span><span class="p">[</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">nCB</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;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">cellFilter</span><span class="p">.</span><span class="n" style="color: #333;">cr2maxCellInd</span><span class="p">)];</span><span class="c1" style="color: #998; font-style: italic;">//robust estimate of the max UMI</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">nUMImin</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;">nUMImax</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">cellFilter</span><span class="p">.</span><span class="n" style="color: #333;">cr2maxMinRatio</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC23" 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;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">cellFilter</span><span class="p">.</span><span class="n" style="color: #333;">type</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="s" style="color: #d14;">"TopCells"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">nUMImin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nUMIperCBsorted</span><span class="p">[</span><span class="n" style="color: #333;">m<span class="idiff left right">ax</span></span><span class="p">(</span><span class="n" style="color: #333;">nCB</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;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">cellFilter</span><span class="p">.</span><span class="n" style="color: #333;">topCells</span><span class="p">)];</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">nUMImin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nUMIperCBsorted</span><span class="p">[</span><span class="n" style="color: #333;">m<span class="idiff left right">in</span></span><span class="p">(</span><span class="n" style="color: #333;">nCB</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;">pSolo</span><span class="p">.</span><span class="n" style="color: #333;">cellFilter</span><span class="p">.</span><span class="n" style="color: #333;">topCells</span><span class="p">)];</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">nUMImin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nUMImin</span><span class="p">,(</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//cannot be zero</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#afd85a07c3f509b173703f2140b578a707ada9e6"><strong>source/Transcript.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,7 +68,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">intScore</span> <span class="n" style="color: #333;">alignScore</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;">Read1</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;">G</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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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variationAdjust</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Genome</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mapGen</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;">R</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">generateCigarP</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">//generates CIGAR</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mSta</span><span class="p">,</span> <span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">peOverlapSEtoPE</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mSta</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Transcript</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">extractSpliceJunctions</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">array</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint64</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sjOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">annotYes</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">chrStartLengthExtended</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/-/commit/ababb9e70de3862cdd3b1353d0c26b48130eaf70#eef122fda3a846cd84614a07011c0a84a375639b"><strong>source/Transcript_alignScore.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 +5,10 @@ intScore Transcript::alignScore(char **Read1, char *G, Parameters &P) {//re-calc</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"> <span class="n" style="color: #333;">maxScore</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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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">nMM</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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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">nMatch</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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nExons</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="LC10" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">maxScore</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"> <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;">R</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Read1</span><span class="p">[</span><span class="n" style="color: #333;">roStr</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;">0</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC13" 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;">iex</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;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span><span class="n" style="color: #333;">iex</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="LC14" 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;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_L</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="LC1" class="line" lang="plaintext">#define STAR_VERSION "2.7.<span class="idiff left right">5c</span>"</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "2.7.<span class="idiff left right">6a</span>"</span></pre>
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