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GitLab

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<h3>

Sascha Steinbiss pushed to branch master

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/2421a62d4a8f3b37efa1d64cdba25e2b987d252f">2421a62d</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-05-07T15:08:52+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.6.0b+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/bd1d8c76457d5f84b56710c386beffbc5c24e302">bd1d8c76</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-05-07T15:08:53+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.6.0b+dfsg'

Update to upstream version '2.6.0b+dfsg'

with Debian dir bcfed05863ebef2d286b705da7977e012d8ba133</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/6188b6b307645af2c9d5ecf239d0a06749264345">6188b6b3</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2018-05-07T15:13:44+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#6e7e9199db44be8b0f606c7c21db10763fc8b0eb">

source/Parameters.cpp

</a>

</li>

<li class="file-stats">

<a href="#e567212bd90532effae5cceb340251e161d1e96e">

source/ReadAlign_chimericDetectionOldOutput.cpp

</a>

</li>

<li class="file-stats">

<a href="#188667251bde9bacea8550ecde93b515b078a8a4">

source/ReadAlign_peOverlapMergeMap.cpp

</a>

</li>

<li class="file-stats">

<a href="#46ef577d4524cc6123d3e3cfa053a5ca85c35274">

source/VERSION

</a>

</li>

<li class="file-stats">

<a href="#add4f105ee2dbb93ee614439a399bb1166d8e20e">

source/Variation.cpp

</a>

</li>

<li class="file-stats">

<a href="#fdaa7fa04b5df2156529588a130b2ee5ff1ed74b">

source/Variation.h

</a>

</li>

<li class="file-stats">

<a href="#185529fd3e0de8506501bfdb392ec98419331b5f">

source/parametersDefault.xxd

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.0b 2018/05/02</span></span>

</pre>

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

2

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<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>

</pre>

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3

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

</pre>

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4

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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 2.5.0a.</span>

</pre>

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5

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

</pre>

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6

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

</pre>

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1

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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 2.6.0a 2018/04/23</span></span>

</pre>

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2

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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>

</pre>

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3

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9

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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="LC9" class="line" lang="markdown"></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rna-star (2.6.0b+dfsg-1) unstable; urgency=medium</span>

</pre>

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

</pre>

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3

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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="plaintext">  * New upstream release.</span>

</pre>

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4

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

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org>  Mon, 07 May 2018 15:09:13 +0200</span>

</pre>

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

</pre>

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1

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">rna-star (2.6.0a+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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8

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

</pre>

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3

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

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  [ Sascha Steinbiss ]</span>

</pre>

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<br>

</li>

<li id="6e7e9199db44be8b0f606c7c21db10763fc8b0eb">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#6e7e9199db44be8b0f606c7c21db10763fc8b0eb"><strong>source/Parameters.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="887" style="width: 35px; color: rgba(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="887" style="width: 35px; color: rgba(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">@@ -887,7 +887,14 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<td class="diff-line-num old_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<td class="diff-line-num new_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<pre style="margin: 0;"> <span id="LC887" 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 --waspOutputMode ... and --varVCFfile /path/to/file.vcf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<td class="diff-line-num new_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

888

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<pre style="margin: 0;"> <span id="LC888" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

<td class="diff-line-num new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

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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="LC889" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

890

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<td class="diff-line-num new_line old" data-linenumber="890" style="width: 35px; color: rgba(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="LC890" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(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="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

890

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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="LC890" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(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="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

891

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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="LC891" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

892

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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wasp</span><span class="p">.</span><span class="n" style="color: #333;">yes</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outSAMtype</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;">"BAM"</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

893

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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp">        <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

894

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<pre style="margin: 0;">+<span id="LC894" 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: --waspOutputMode requires output to BAM file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

895

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<pre style="margin: 0;">+<span id="LC895" 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 --waspOutputMode ... and --outSAMtype BAM ... </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

896

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<pre style="margin: 0;">+<span id="LC896" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

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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="LC897" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

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<td class="diff-line-num new_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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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="LC898" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

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<td class="diff-line-num new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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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="LC899" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//outSAMattributes</span></span>

</pre>

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893

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<td class="diff-line-num new_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp">    <span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">NH</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//TODO re-write as class with constructor?</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1050" style="width: 35px; color: rgba(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="1057" style="width: 35px; color: rgba(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">@@ -1050,7 +1057,7 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<td class="diff-line-num old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

</td>

<td class="diff-line-num new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1057

</td>

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

<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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

</td>

<td class="diff-line-num new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

</td>

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

<pre style="margin: 0;"> <span id="LC1058" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

</td>

<td class="diff-line-num new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1059

</td>

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

<pre style="margin: 0;"> <span id="LC1059" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1053

</td>

<td class="diff-line-num new_line old" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1053" class="line" lang="cpp"><span class="idiff left right">    </span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1060

</td>

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

<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

</td>

<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

</td>

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

<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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1055

</td>

<td class="diff-line-num new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1062

</td>

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

<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>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1056

</td>

<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

</td>

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

<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>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1058" style="width: 35px; color: rgba(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="1065" style="width: 35px; color: rgba(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">@@ -1058,6 +1065,24 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<td class="diff-line-num old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

</td>

<td class="diff-line-num new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1065

</td>

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

<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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1059

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC1066" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1060

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC1067" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1068

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp">                <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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: --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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<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 --chimOutType WithinBAM</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC1080" 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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC1081" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1082

</td>

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

<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1083

</td>

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

<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp">        </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1084

</td>

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

<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1085

</td>

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

<pre style="margin: 0;">+<span id="LC1085" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

</td>

<td class="diff-line-num new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1086

</td>

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

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1062

</td>

<td class="diff-line-num new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1087

</td>

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

<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>

</pre>

</td>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1088

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1217" style="width: 35px; color: rgba(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="1242" style="width: 35px; color: rgba(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">@@ -1217,8 +1242,8 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<td class="diff-line-num old_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1217

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<td class="diff-line-num new_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1242

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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1218

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<td class="diff-line-num new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1243

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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gLoad</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">"NoSharedMemory"</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1219

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<td class="diff-line-num new_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1244

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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp">            <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">errOut</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1220

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<td class="diff-line-num new_line old" data-linenumber="1245" style="width: 35px; color: rgba(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="LC1220" 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: 2-pass method is not compatible with <span class="idiff left right">pGe.gLoad<<</span>"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gLoad</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1221

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<td class="diff-line-num new_line old" data-linenumber="1245" style="width: 35px; color: rgba(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="LC1221" 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 --genomeLoad NoSharedMemory ; this is the only <span class="idiff left right">compatible option at the moment.s</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(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="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1245

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<pre style="margin: 0;">+<span id="LC1245" 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: 2-pass method is not compatible with <span class="idiff left right">--genomeLoad </span>"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">pGe</span><span class="p">.</span><span class="n" style="color: #333;">gLoad</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(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="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1246

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<pre style="margin: 0;">+<span id="LC1246" 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 --genomeLoad NoSharedMemory ; this is the only <span class="idiff left right">option compatible with --twopassMode Basic .</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1222

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<td class="diff-line-num new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1247

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<pre style="margin: 0;"> <span id="LC1247" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1223

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<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1248

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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="cpp">        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1224

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<td class="diff-line-num new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1249

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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="cpp">        <span class="n" style="color: #333;">twoPass</span><span class="p">.</span><span class="n" style="color: #333;">yes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1359" style="width: 35px; color: rgba(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="1384" style="width: 35px; color: rgba(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">@@ -1359,6 +1384,8 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters</td>

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<td class="diff-line-num old_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1359

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<td class="diff-line-num new_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1384

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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//peOverlap</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1360

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<td class="diff-line-num new_line" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1385

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<pre style="margin: 0;"> <span id="LC1385" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1361

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<td class="diff-line-num new_line" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1386

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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="cpp">        <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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1362" style="width: 35px; color: rgba(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="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1387

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<pre style="margin: 0;">+<span id="LC1387" 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="1388" style="width: 35px; color: rgba(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="LC1388" class="line" lang="cpp">        <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="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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1389

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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">////////////////////////////////////////////////</span></span>

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<br>

</li>

<li id="e567212bd90532effae5cceb340251e161d1e96e">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#e567212bd90532effae5cceb340251e161d1e96e"><strong>source/ReadAlign_chimericDetectionOldOutput.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">@@ -78,7 +78,7 @@ void ReadAlign::chimericDetectionOldOutput() {</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="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp">            <span class="n" style="color: #333;">bamN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">],</span>  <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">mateChr</span></span><span class="p">],</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">,</span> \</span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">            <span class="n" style="color: #333;">bamN</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">alignBAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">itr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">],</span>  <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">mateChr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mapGen</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nChrReal</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">mateChr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>],</span> <span class="n" style="color: #333;">mateStrand</span><span class="p">,</span> \</span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">                            <span class="n" style="color: #333;">alignType</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrOrder</span><span class="p">,</span> <span class="n" style="color: #333;">outBAMoneAlign</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</span><span class="p">,</span> <span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bamN</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">            <span class="n" style="color: #333;">bamBytesTotal</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outBAMoneAlignNbytes</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span><span class="c1" style="color: #998; font-style: italic;">//outBAMoneAlignNbytes[1] = 0 if SE is recorded</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">        <span class="p">};</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(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">@@ -110,39 +110,43 @@ void ReadAlign::chimericDetectionOldOutput() {</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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

112

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

112

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC113" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC114" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimN</span><span class="p">;</span><span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC115" class="line" lang="cpp">    <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//write all chimeric pieces to Chimeric.out.sam/junction</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC116" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmates</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//PE: need mate info</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

117

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC117" class="line" lang="cpp">            <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

118

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC118" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

119

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC119" class="line" lang="cpp">            <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//the other segment has 2 mates, need to find the opposite mate</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

120

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC120" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(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="LC121" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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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="LC113" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">samOld</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">chimN</span><span class="p">;</span><span class="n" style="color: #333;">iTr</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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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="LC115" class="line" lang="cpp">        <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//write all chimeric pieces to Chimeric.out.sam/junction</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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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="LC116" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">readNmates</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//PE: need mate info</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp">                <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span> <span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" class="line" lang="cpp">                <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//the other segment has 2 mates, need to find the opposite mate</span></span>

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

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">                        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">                    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">                <span class="p">};</span></span>

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<td class="diff-line-num new_line old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp">            <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp">            <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp">            <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">            <span class="idiff left right">    </span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateChr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">            <span class="idiff left right">    </span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">mateStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="cpp">            <span class="idiff left right">    </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mateStrand</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">Str</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">iTr</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="n" style="color: #333;">EX_iFrag</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp">            <span class="n" style="color: #333;">outputTranscriptSAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">],</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="n" style="color: #333;">mateStrand</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="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chunkOutChimSAM</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> </span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(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="LC133" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp">            <span class="n" style="color: #333;">outputTranscriptSAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">],</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chunkOutChimSAM</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(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="LC131" class="line" lang="cpp">                <span class="n" style="color: #333;">outputTranscriptSAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">],</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="n" style="color: #333;">mateChr</span><span class="p">,</span> <span class="n" style="color: #333;">mateStart</span><span class="p">,</span> <span class="n" style="color: #333;">mateStrand</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="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chunkOutChimSAM</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="cpp">                <span class="n" style="color: #333;">outputTranscriptSAM</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="n" style="color: #333;">iTr</span><span class="p">],</span> <span class="n" style="color: #333;">chimN</span><span class="p">,</span> <span class="n" style="color: #333;">iTr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chunkOutChimSAM</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="cpp">            <span class="p">};</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//junction + SAMp</span></span>

</pre>

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138

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(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="LC138" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimJ0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Str</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="s" style="color: #d14;">"+"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(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="LC139" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimJ1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"+"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> \</span>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(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="LC140" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimMotif</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimRepeat0</span>  <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimRepeat1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">readName</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outputTranscriptCIGARp</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> \</span>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span>  <span class="n" style="color: #333;">outputTranscriptCIGARp</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(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="LC143" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrRG</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">readFilesIndex</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span><span class="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 class="c1" style="color: #998; font-style: italic;">//<<"\t"<< trChim[0].exons[0][EX_iFrag]+1 --- no need for that, since trChim[0] is always on the first mate</span></span>

</pre>

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

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

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">pCh</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">junctions</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//junction + SAMp</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimJ0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Str</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="s" style="color: #d14;">"+"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> \</span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">                <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrName</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimJ1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"+"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> \</span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">                <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimMotif</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimRepeat0</span>  <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chimRepeat1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">readName</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> \</span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp">                <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outputTranscriptCIGARp</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> \</span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp">                <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">EX_G</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mapGen</span><span class="p">.</span><span class="n" style="color: #333;">chrStart</span><span class="p">[</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">Chr</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span>  <span class="n" style="color: #333;">outputTranscriptCIGARp</span><span class="p">(</span><span class="n" style="color: #333;">trChim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrPresent</span><span class="p">.</span><span class="n" style="color: #333;">RG</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">outSAMattrRG</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">readFilesIndex</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chunkOutChimJunction</span> <span class="o" style="font-weight: 600;"><<</span><span class="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 class="c1" style="color: #998; font-style: italic;">//<<"\t"<< trChim[0].exons[0][EX_iFrag]+1 --- no need for that, since trChim[0] is always on the first mate</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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

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

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<br>

</li>

<li id="188667251bde9bacea8550ecde93b515b078a8a4">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#188667251bde9bacea8550ecde93b515b078a8a4"><strong>source/ReadAlign_peOverlapMergeMap.cpp</strong></a>

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

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></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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<pre style="margin: 0;"> <span id="LC7" 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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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"></span>

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

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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">@@ -18,10 +18,9 @@ void ReadAlign::peOverlapMergeMap() {</td>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp">    <span 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="LC19" 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="LC20" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp">    </span>

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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="LC24" 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="LC25" class="line" lang="cpp">    <span class="p">};</span></span>

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(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="73" style="width: 35px; color: rgba(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">@@ -74,6 +73,8 @@ void ReadAlign::peOverlapMergeMap() {</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">    </span>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(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="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="LC75" 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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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC76" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(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="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>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">    </span>

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

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" style="width: 35px; color: rgba(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="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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,12 +203,13 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig</td>

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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;">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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<pre style="margin: 0;"> <span id="LC205" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(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="LC205" 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><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;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(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="LC206" 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><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;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(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="LC207" 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><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;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(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="LC208" 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><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;">t</span><span class="p">.</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC209" 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><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;">t</span><span class="p">.</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(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="LC210" class="line" lang="cpp"></span>

</pre>

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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;">nExons</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;">iex</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="211" style="width: 35px; color: rgba(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="207" style="width: 35px; color: rgba(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="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><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;">t</span><span class="p">.</span><span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="211" style="width: 35px; color: rgba(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="208" style="width: 35px; color: rgba(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="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><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;">t</span><span class="p">.</span><span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(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="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><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;">t</span><span class="p">.</span><span class="n" style="color: #333;">sjStr</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="211" style="width: 35px; color: rgba(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="210" style="width: 35px; color: rgba(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="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><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="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">-</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>

</pre>

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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><span class="mi" style="color: #099;">1</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;">t</span><span class="p">.</span><span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">iex</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">            <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//record these exons for mate2</span></span>

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<pre style="margin: 0;"> <span id="LC214" 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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<pre style="margin: 0;"> <span id="LC215" 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_G</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_G</span><span class="p">];</span>  </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" style="width: 35px; color: rgba(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">@@ -227,8 +229,11 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig</td>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nExons</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">        <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">        <span class="n" style="color: #333;">canonSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//marks "junction" between mates</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">        <span class="n" style="color: #333;">sjAnnot</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC233" 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><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC234" 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><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="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">        <span class="n" style="color: #333;">shiftSJ</span><span class="p">[</span><span class="n" style="color: #333;">nExons</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">    <span class="p">};</span> </span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//copy scalar variables</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">;</span><span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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</li>

<li id="46ef577d4524cc6123d3e3cfa053a5ca85c35274">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#46ef577d4524cc6123d3e3cfa053a5ca85c35274"><strong>source/VERSION</strong></a>

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1

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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">a</span>"</span></pre>

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1

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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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</li>

<li id="add4f105ee2dbb93ee614439a399bb1166d8e20e">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#add4f105ee2dbb93ee614439a399bb1166d8e20e"><strong>source/Variation.cpp</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,9 @@ Variation::Variation (Parameters &Pin, vector <uint> &chrStartIn, map <string,ui</td>

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12

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12

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp">    <span class="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="LC14" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="cpp">    <span class="n" style="color: #333;">varOutFileName</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;">outFileNamePrefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Variation.out"</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp">    <span class="n" style="color: #333;">varOutStream</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">varOutFileName</span><span class="p">);</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//not used yet</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//varOutFileName=P.outFileNamePrefix+"Variation.out";</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//varOutStream.open(varOutFileName);</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">    <span class="n" style="color: #333;">vcfFile</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;">var</span><span class="p">.</span><span class="n" style="color: #333;">vcfFile</span><span class="p">;</span></span>

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

</pre>

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<br>

</li>

<li id="fdaa7fa04b5df2156529588a130b2ee5ff1ed74b">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#fdaa7fa04b5df2156529588a130b2ee5ff1ed74b"><strong>source/Variation.h</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,8 +42,8 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c">    </span>

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">vcfFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">varOutFileName</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(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="LC46" class="line" lang="c">    <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">varOutStream</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//output file for variations</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(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="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>string varOutFileName;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(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="46" style="width: 35px; color: rgba(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="LC46" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>ofstream varOutStream;//output file for variations</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="c">    </span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c">    <span class="n" style="color: #333;">vector</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrStart</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//this needs to be replaced with a structure that contains basic genome variables</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c">    <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span><span class="n" style="color: #333;">uint</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrNameIndex</span><span class="p">;</span></span>

</pre>

</td>

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<li id="185529fd3e0de8506501bfdb392ec98419331b5f">

<a href="https://salsa.debian.org/med-team/rna-star/compare/58bcf9d3f20545e416d52e58bfaa66922754ab84...6188b6b307645af2c9d5ecf239d0a06749264345#185529fd3e0de8506501bfdb392ec98419331b5f"><strong>source/parametersDefault.xxd</strong></a>

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