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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/rna-star">Debian Med / rna-star</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb">7511af81</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-05-16T08:38:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.6.0c+dfsg</pre>
</li>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
</li>
<li class="file-stats">
<a href="#6e7e9199db44be8b0f606c7c21db10763fc8b0eb">
source/Parameters.cpp
</a>
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<li class="file-stats">
<a href="#188667251bde9bacea8550ecde93b515b078a8a4">
source/ReadAlign_peOverlapMergeMap.cpp
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<li class="file-stats">
<a href="#8ddf1f0debf2582831408d52143450b1ba6e1117">
source/ReadAlign_waspMap.cpp
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<li class="file-stats">
<a href="#4896a67af34962395106d0bd2c41b227ffde5a58">
source/STAR.cpp
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<li class="file-stats">
<a href="#fe90b02c2a1b9c4383b00f761ae92e70b34253ac">
source/SequenceFuns.cpp
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<li class="file-stats">
<a href="#aee0d11f6c0e6bc020b1dc5c0773e66662064dd7">
source/SequenceFuns.h
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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/7511af817f731678c350c9d4267755e19bc5ebbb#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.0c 2018/05/10</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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></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"><span class="p">*</span> Fixed bugs in merging mates (--peOverlap<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>) and WASP filtering algorithms. Please see CHANGES and RELEASEnotes from 2.6.0a.</span>
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5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.0b 2018/05/02</span></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">*</span> Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.<span class="idiff left right">5</span>.0a.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.<span class="idiff left right">6</span>.0a.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.0a 2018/04/23</span></span>
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<li id="6e7e9199db44be8b0f606c7c21db10763fc8b0eb">
<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#6e7e9199db44be8b0f606c7c21db10763fc8b0eb"><strong>source/Parameters.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1039" style="width: 35px; color: rgba(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="1039" style="width: 35px; color: rgba(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">@@ -1039,75 +1039,76 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>
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<td class="diff-line-num old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1039
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<td class="diff-line-num new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="cpp"> <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="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_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1040
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<td class="diff-line-num new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"> <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="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_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1041
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<td class="diff-line-num new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp"> <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="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//default</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1042
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="LC1042" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type1</span> <span class="o" style="font-weight: 600;">:</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;">type</span><span class="p">)</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"WithinBAM"</span><span class="p">)</span> <span class="p">{</span></span>
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1044
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="LC1044" class="line" lang="cpp"> <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="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="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1045
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">type</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;">"SeparateSAMold"</span><span class="p">)</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="1042" style="width: 35px; color: rgba(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="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="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="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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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">type</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;">"Junctions"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1048
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="LC1048" class="line" lang="cpp"> <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="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="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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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"HardClip"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1050
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="LC1050" class="line" lang="cpp"> <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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1051
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="LC1051" 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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"SoftClip"</span><span class="p">)</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="1042" style="width: 35px; color: rgba(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;">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="nb" style="color: #0086b3;">false</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="1042" style="width: 35px; color: rgba(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 class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1054
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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 class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>
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1055
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<td class="diff-line-num new_line old" data-linenumber="1042" style="width: 35px; color: rgba(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="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 value for --chimOutType: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">type1</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="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="1042" style="width: 35px; color: rgba(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="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 --chimOutType Junctions , SeparateSAMold , WithinBAM , HardClip </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="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="1042" style="width: 35px; color: rgba(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;">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 old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">segmentMin</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;">//only if chimeric detection is activated</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type1</span> <span class="o" style="font-weight: 600;">:</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;">type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"WithinBAM"</span><span class="p">)</span> <span class="p">{</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <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="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="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" 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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"SeparateSAMold"</span><span class="p">)</span> <span class="p">{</span></span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <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="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="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" 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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Junctions"</span><span class="p">)</span> <span class="p">{</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <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="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="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1050
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<pre style="margin: 0;">+<span id="LC1050" 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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"HardClip"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <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="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="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1052
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<pre style="margin: 0;">+<span id="LC1052" 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;">type1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"SoftClip"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <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="nb" style="color: #0086b3;">false</span><span class="p">;</span> </span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" 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="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
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<pre style="margin: 0;">+<span id="LC1055" 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="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
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<pre style="margin: 0;">+<span id="LC1056" 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 value for --chimOutType: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">type1</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="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
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<pre style="margin: 0;">+<span id="LC1057" 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 --chimOutType Junctions , SeparateSAMold , WithinBAM , HardClip </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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1058
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<pre style="margin: 0;">+<span id="LC1058" 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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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="p">};</span></span>
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1058
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="cpp"> <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>
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1060
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="cpp"></span>
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1061
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">&&</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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1062
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<pre style="margin: 0;">-<span id="LC1062" 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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1063
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1063" 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: --chimOutType WithinBAM 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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<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="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">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1064" 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 --outSAMtype BAM Unsorted/SortedByCoordinate</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="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1065
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1065" 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="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1066
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="cpp"> <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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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1068
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1068" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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><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="o" style="font-weight: 600;">||</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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<td class="diff-line-num old old_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1069
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1069" 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="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="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">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1070" 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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<td class="diff-line-num old old_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1071
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<td class="diff-line-num new_line old" 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">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1071" 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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<td class="diff-line-num old old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1072
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1072" 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="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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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1073" class="line" lang="cpp"> <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="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">
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1075
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">NbasesMin</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1076
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1076" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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><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="o" style="font-weight: 600;">||</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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<td class="diff-line-num new old_line" data-linenumber="1077" style="width: 35px; color: rgba(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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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">&&</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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<td class="diff-line-num old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1077
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<td class="diff-line-num new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<pre style="margin: 0;"> <span id="LC1063" 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="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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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1078" 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: --chim<span class="idiff left right">MultimapNmax 0 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType 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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<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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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1079" 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 --<span class="idiff left right">chimOutType 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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1064
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<pre style="margin: 0;">+<span id="LC1064" 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: --chim<span class="idiff left right">OutType WithinBAM requires BAM output</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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<td class="diff-line-num new new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1065
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<pre style="margin: 0;">+<span id="LC1065" 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 --<span class="idiff left right">outSAMtype BAM Unsorted/SortedByCoordinate</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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<td class="diff-line-num old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1080
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<td class="diff-line-num new_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1066
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<pre style="margin: 0;"> <span id="LC1066" 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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1081
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<td class="diff-line-num new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1067
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="cpp"> <span class="p">};</span></span>
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1082
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="p">};</span></span>
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1083
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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>
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1084
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1084" class="line" lang="cpp"> </span>
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1085
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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>
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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="k" style="font-weight: 600;">if</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="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;">NM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1087
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="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_NM</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="1068" style="width: 35px; color: rgba(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;">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 --chimOutType=WithinBAM, therefore STAR will output NM 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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1089
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="cpp"> <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>
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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="1068" style="width: 35px; color: rgba(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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">genomicN</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="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="1068" style="width: 35px; color: rgba(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="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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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>
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1093
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1094
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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;">"banGenomicN"</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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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1095" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1096
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1096" class="line" lang="cpp"> <span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">genomicN</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="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1097
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1097" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1098
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1098" class="line" lang="cpp"> <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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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;">"None"</span><span class="p">)</span></span>
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1099
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<td class="diff-line-num new_line old" data-linenumber="1068" style="width: 35px; color: rgba(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="LC1099" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//nothing to do</span></span>
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1100
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="cpp"> <span class="p">}</span></span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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><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="o" style="font-weight: 600;">||</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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<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" 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="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
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<pre style="margin: 0;">+<span id="LC1071" 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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<td class="diff-line-num new new_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
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<pre style="margin: 0;">+<span id="LC1072" 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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<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" 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="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">NbasesMin</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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><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="o" style="font-weight: 600;">||</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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<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" 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="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" 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 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType WithinBAM</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="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" 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 WithinBAM</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="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" 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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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"> <span class="p">};</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="p">};</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="cpp"></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="cpp"></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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;">NM</span><span class="p">)</span> <span class="p">{</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" 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 new new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" 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 --chimOutType=WithinBAM, therefore STAR will output NM 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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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="p">};</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">genomicN</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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1093
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<pre style="margin: 0;">+<span id="LC1093" 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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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>
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1102
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="cpp"> <span class="p">{</span></span>
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1103
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<pre style="margin: 0;">-<span id="LC1103" 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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1104
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1104" 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: unrecognized value of --chimFilter="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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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1105
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1105" 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: use allowed values: banGenomicN || None"</span><span class="p">;</span></span>
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1106
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC1106" 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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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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;">"banGenomicN"</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>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">genomicN</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="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"> <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;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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;">"None"</span><span class="p">)</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//nothing to do</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <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="k" style="font-weight: 600;">else</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="cpp"> <span class="p">{</span></span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" 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="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" 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: unrecognized value of --chimFilter="</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">stringIn</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="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1106
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<pre style="margin: 0;">+<span id="LC1106" 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: use allowed values: banGenomicN || None"</span><span class="p">;</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" 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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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> <span class="p">};</span></span>
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1107
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp"> <span class="p">};</span></span>
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1108
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp"> <span class="p">};</span></span>
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1109
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp"></span>
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1110
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<pre style="margin: 0;">-<span id="LC1110" class="line" lang="cpp"></span>
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1111
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1112
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<pre style="margin: 0;"> <span id="LC1112" 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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1112
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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;">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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1113
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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;">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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<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#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">@@ -3,10 +3,9 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>
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4
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4
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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;">ReadAlign</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">peOverlapMergeMap</span><span class="p">()</span> <span class="p">{</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"> </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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6
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<pre style="margin: 0;"> <span id="LC6" 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;">P</span><span class="p">.</span><span class="n" style="color: #333;">peOverlap</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;">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;">//no peOverlap</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">peOv</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;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">peOv</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;">false</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="LC11" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//debug</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(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">@@ -17,10 +16,10 @@ void ReadAlign::peOverlapMergeMap() {</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">copyRead</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="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">peMergeRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">peMergeMates</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;">peOv</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;">peOv</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;">peOv</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;">false</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">nOv</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;">//check if mates can be merged, if not - return</span></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;">//cout <<"\n-1\n";</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">peOv</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;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" 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="LC24" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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">@@ -36,7 +35,6 @@ void ReadAlign::peOverlapMergeMap() {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cout <<P.genomeNumToNT[peMergeRA->Read1[0][ii]];</span></span>
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<pre style="margin: 0;"> <span id="LC36" 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="LC37" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cout << "\n";</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC38" 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="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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,10 +69,8 @@ void ReadAlign::peOverlapMergeMap() {</td>
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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="c1" style="color: #998; font-style: italic;">//P.alignSplicedMateMapLminOverLmate=P_alignSplicedMateMapLminOverLmate;</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="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">peScore</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">chimRecord</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">peScore</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">chimRecord</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//otherwise peOv.yes=false</span></span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">peOv</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC76" 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="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">peOv</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;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <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="k" style="font-weight: 600;">return</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">@@ -82,8 +78,8 @@ void ReadAlign::peOverlapMergeMap() {</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC79" 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;">peMergeMates</span><span class="p">()</span> <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="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localSearch</span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="n" style="color: #333;">Read1</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;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">readLength</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">MMp</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="n" style="color: #333;">s0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localSearch</span><span class="p">(</span><span class="n" style="color: #333;">Read1</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;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">readLength</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">Read1</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">MMp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">s1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localSearch<span class="idiff left right">NisMM</span></span><span class="p">(</span><span class="n" style="color: #333;">Read1</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="n" style="color: #333;">Read1</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;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">readLength</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">MMp</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;">uint</span> <span class="n" style="color: #333;">s0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">localSearch<span class="idiff left right">NisMM</span></span><span class="p">(</span><span class="n" style="color: #333;">Read1</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;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">readLength</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">Read1</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">peOverlap</span><span class="p">.</span><span class="n" style="color: #333;">MMp</span><span class="p">);</span></span>
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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="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">o1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min</span><span class="p">(</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="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;">s1</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;">uint</span> <span class="n" style="color: #333;">o0</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min</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="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="n" style="color: #333;">s0</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(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">@@ -203,12 +199,12 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig</td>
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203
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"></span>
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204
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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;">exons</span><span class="p">[</span><span class="n" style="color: #333;">nExons</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="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;">t</span><span class="p">.</span><span class="n" style="color: #333;">Str</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">Str</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="p">][</span><span class="n" style="color: #333;">EX_sjA</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">t</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_sjA</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">nExons</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="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">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</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;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">canonSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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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;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sjAnnot</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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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;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sjStr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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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;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">shiftSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">shiftSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">iex</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nExons</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" 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="p"><span class="idiff left">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">canonSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">iex</span></span><span class="p">];</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="p"><span class="idiff left">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sjAnnot</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">iex</span></span><span class="p">];</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;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="p"><span class="idiff left">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sjStr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">iex</span></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;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="p"><span class="idiff left">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">shiftSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">iex</span></span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="p"><span class="idiff left">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">shiftSJ</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">iex</span></span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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212
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="p">};</span></span>
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213
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//record these exons for mate2</span></span>
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214
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</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_R</span><span class="p">]</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;">imate</span><span class="p">])</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//exon left is inside the mate</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#8ddf1f0debf2582831408d52143450b1ba6e1117"><strong>source/ReadAlign_waspMap.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">@@ -61,7 +61,9 @@ void ReadAlign::waspMap() {</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <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>
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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;">waspRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mapOneRead</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">waspRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">multMapSelect</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;">waspRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mappedFilter</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">waspRA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unmapType</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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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">waspType</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="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#4896a67af34962395106d0bd2c41b227ffde5a58"><strong>source/STAR.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">@@ -48,6 +48,18 @@ void usage() {</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argInN</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argIn</span><span class="p">[])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> </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;">//debug</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;">// uint nn=4000000000;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uint* dummy=new uint[nn];</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// std::cout <<"Allocated"<<endl;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// for (uint ii=0;ii<nn;ii++) {</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;">// dummy[ii]=14829735431805718528LLU;;</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;">// };</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;">// std::cout <<"Filled "<<dummy[0]<<endl;</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;">// delete[] dummy; </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;">// std::cout <<"Deleted"<<endl;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> </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;">// If no argument is given, or the first argument is either '-h' or '--help', run usage()</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">argInN</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="p">(</span><span class="n" style="color: #333;">argInN</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="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="s" style="color: #d14;">"-h"</span><span class="p">,</span><span class="n" style="color: #333;">argIn</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">strcmp</span> <span class="p">(</span><span class="s" style="color: #d14;">"--help"</span><span class="p">,</span><span class="n" style="color: #333;">argIn</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 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;">usage</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">@@ -201,6 +201,32 @@ uint localSearch(const char *x, uint nx, const char *y, uint ny, double pMM){</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ixBest</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">localSearchNisMM</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">x</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">y</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">ny</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pMM</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//find the best alignment of two short sequences x and y</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//pMM is the maximum percentage of mismatches</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Ns in x OR y are considered mismatches</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <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 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 class="n" style="color: #333;">nMatchBest</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;">nMMbest</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;">ixBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nx</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC209" 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;">ix</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;">ix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nx</span><span class="p">;</span><span class="n" style="color: #333;">ix</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="LC210" 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 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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<pre style="margin: 0;">+<span id="LC211" 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;">iy</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;">iy</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">ny</span><span class="p">,</span><span class="n" style="color: #333;">nx</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ix</span><span class="p">);</span><span class="n" style="color: #333;">iy</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="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">ix</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">iy</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">iy</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">iy</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">nMatch</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC214" 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="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">nMM</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span> <span class="n" style="color: #333;">nMatch</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">nMatchBest</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">nMatch</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">nMatchBest</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nMM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nMMbest</span><span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">(</span><span class="n" style="color: #333;">nMM</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">(</span><span class="n" style="color: #333;">nMatch</span><span class="p">)</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">pMM</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">ixBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">nMatchBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nMatch</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">nMMbest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nMM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <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;">return</span> <span class="n" style="color: #333;">ixBest</span><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="LC230" class="line" lang="cpp"><span class="n" style="color: #333;">uint</span> <span class="nf" style="color: #900; font-weight: 600;">qualitySplit</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 class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">q</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">Qsplit</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">maxNsplit</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">minLsplit</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;">splitR</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//splits the read r[L] by quality scores q[L], outputs in splitR - split coordinate/length - per base</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//returns number of good split regions</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#aee0d11f6c0e6bc020b1dc5c0773e66662064dd7"><strong>source/SequenceFuns.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,8 @@ char convertNt01234(const char R0);//transform sequence from ACGT into 0-1-2-3-</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">chrFind</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// find chromosome from global locus</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">localSearch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//local search to clip adapter</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">localSearchNisMM</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">x</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">y</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">ny</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pMM</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">qualitySplit</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">**</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb#46ef577d4524cc6123d3e3cfa053a5ca85c35274"><strong>source/VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "STAR_2.6.0<span class="idiff left right">b</span>"</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "STAR_2.6.0<span class="idiff left right">c</span>"</span></pre>
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