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<h3>
Steffen Möller 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/ced0e9fbd2d93eb0d0a4128050a19ff6c8167c59">ced0e9fb</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:28:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.6.1c+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/8cb1fe86953bad8a334f8fe018b4efa0bcbe701b">8cb1fe86</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:28:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.6.1c+dfsg'
Update to upstream version '2.6.1c+dfsg'
with Debian dir 3b8d560389d521ad76eba1fee17ecff271c06bae</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/264871e9943fddb8af60dd34b2e523a579a57d74">264871e9</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:29:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for new upstream version.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/830c815a780f79edcea5d2d2eeaef6f29228f75a">830c815a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:31:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.6.1c+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rna-star/commit/6c0fc528f72f6a6842d90ba18fd9875c002900fc">6c0fc528</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:31:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.6.1c+dfsg'
Update to upstream version '2.6.1c+dfsg'
with Debian dir 4ed65df0d4142e45dd1cbdadfe182f6bb03e235a</pre>
</li>
</ul>
<h4>6 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="#32c87d85b8e6a7f392241db417a7cd034f3e79d7">
source/ReadAlign_chimericDetectionPEmerged.cpp
</a>
</li>
<li class="file-stats">
<a href="#fe90b02c2a1b9c4383b00f761ae92e70b34253ac">
source/SequenceFuns.cpp
</a>
</li>
<li class="file-stats">
<a href="#46ef577d4524cc6123d3e3cfa053a5ca85c35274">
source/VERSION
</a>
</li>
<li class="file-stats">
<a href="#8d3b9ff64d8dd5569149f7e7f75554bcab49ad30">
source/readLoad.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.1c 2018/10/17</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======================</span></span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">*</span> Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.</span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">STAR 2.6.1b 2018/09/06</span></span>
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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;">======================</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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="LC8" 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/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rna-star (2.6.1c+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 23 Oct 2018 13:28:51 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">rna-star (2.6.1b+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version.</span>
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<li id="32c87d85b8e6a7f392241db417a7cd034f3e79d7">
<a href="https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#32c87d85b8e6a7f392241db417a7cd034f3e79d7"><strong>source/ReadAlign_chimericDetectionPEmerged.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ void ReadAlign::chimericDetectionPEmerged(ReadAlign &seRA) {</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">segLmin</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">segLmin</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">segLen</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="n" style="color: #333;"><span class="idiff">segLmin</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">trChim</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">exons</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">EX_G</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="n" style="color: #333;"><span class="idiff">trChim</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">exons</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">EX_G</span></span><span class="p"><span class="idiff right">])</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">segLmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">segLen</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">][</span><span class="n" style="color: #333;">jj</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ii</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//trChim of the shortest segment length</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jj</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//mate of the shortest segment length</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#fe90b02c2a1b9c4383b00f761ae92e70b34253ac"><strong>source/SequenceFuns.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(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">@@ -139,7 +139,7 @@ void convertNucleotidesToNumbers(const char* R0, char* R1, const uint Lread) {//</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="p">(</span><span class="mi" style="color: #099;">84</span><span class="p">):</span> <span class="k" style="font-weight: 600;">case</span><span class="p">(</span><span class="mi" style="color: #099;">116</span><span class="p">):</span> </span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">R1</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span><span class="k" style="font-weight: 600;">break</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//T</span></span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="nl">default:</span> </span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">R1</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">9</span></span><span class="p"><span class="idiff">);</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//anything else</span></span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">R1</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left">4</span></span><span class="p"><span class="idiff">);</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//anything else is converted to N</span></span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC145" 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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -160,7 +160,7 @@ uint convertNucleotidesToNumbersRemoveControls(const char* R0, char* R1, const u</td>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">R0</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//control characters are skipped</span></span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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162
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//all non-control non-ACGT characters are convreted to N</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">R1</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//anything else</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">R1</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//anything else</span></span>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="p">};</span></span>
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165
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="p">};</span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iR1</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#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_2.6.1<span class="idiff left right">b</span>"</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#define STAR_VERSION "STAR_2.6.1<span class="idiff left right">c</span>"</span></pre>
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<a href="https://salsa.debian.org/med-team/rna-star/compare/088d0682ff48578120a2295297796e4312daf4e1...6c0fc528f72f6a6842d90ba18fd9875c002900fc#8d3b9ff64d8dd5569149f7e7f75554bcab49ad30"><strong>source/readLoad.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -84,7 +84,7 @@ int readLoad(istream& readInStream, Parameters& P, uint iMate, uint& Lread, uint</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">Lread</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">};</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">convertNucleotidesToNumbers</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip5pNbases</span><span class="p">[</span><span class="n" style="color: #333;">iMate</span><span class="p">],</span><span class="n" style="color: #333;">SeqNum</span><span class="p">,</span><span class="n" style="color: #333;">Lread</span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">convertNucleotidesToNumbers<span class="idiff left right">RemoveControls</span></span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip5pNbases</span><span class="p">[</span><span class="n" style="color: #333;">iMate</span><span class="p">],</span><span class="n" style="color: #333;">SeqNum</span><span class="p">,</span><span class="n" style="color: #333;">Lread</span><span class="p">);</span></span>
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88
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//clip the adapter</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">P</span><span class="p">.</span><span class="n" style="color: #333;">clip3pAdapterSeq</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">iMate</span><span class="p">).</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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