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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/rsem">Debian Med / rsem</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rsem/commit/a87d5923b625c95c335e7664764c07e804107125">a87d5923</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-07-12T19:52:07Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.2+dfsg</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2aef7edfde269b0233cb938e64056f0bb82a43c1">
EM.cpp
</a>
</li>
<li class="file-stats">
<a href="#ef1025cc6f59414d24509fa38c7357a10e37a970">
WriteResults.h
</a>
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<li class="file-stats">
<a href="#5ae6fa11155cf92496c7c4bc847d0d0e467680bf">
rsem-calculate-expression
</a>
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<h4>Changes:</h4>
<li id="2aef7edfde269b0233cb938e64056f0bb82a43c1">
<a href="https://salsa.debian.org/med-team/rsem/commit/a87d5923b625c95c335e7664764c07e804107125#2aef7edfde269b0233cb938e64056f0bb82a43c1"><strong>EM.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">@@ -612,35 +612,59 @@ int main(int argc, char* argv[]) {</td>
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612
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">N0</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">N1</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">N2</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">N_tot</span><span class="p">;</span></span>
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613
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<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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614
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp"></span>
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615
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">general_assert</span><span class="p">(</span><span class="n" style="color: #333;">N1</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"There are no alignable reads!"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
617
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">READ_INT_TYPE</span><span class="p">)</span><span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">N1</span><span class="p">)</span> <span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N1</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
619
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//set model parameters</span></span>
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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
620
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</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;">N0</span><span class="p">;</span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</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;">N1</span><span class="p">;</span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">refs</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="623" style="width: 35px; color: rgba(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="LC623" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="624" style="width: 35px; color: rgba(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="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.mparams"</span><span class="p">,</span> <span class="n" style="color: #333;">imdName</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">);</span></span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp"></span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">general_assert</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Cannot open "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cstrtos</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"It may not exist."</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
629
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">minL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">maxL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">probF</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 0 or 1 , for estRSPD</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">estRSPD</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</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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633
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mate_minL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mate_maxL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">sd</span><span class="p">;</span></span>
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634
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">seedLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="cpp"></span>
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637
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//run EM</span></span>
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638
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">read_type</span><span class="p">)</span> <span class="p">{</span></span>
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639
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SingleRead</span><span class="p">,</span> <span class="n" style="color: #333;">SingleHit</span><span class="p">,</span> <span class="n" style="color: #333;">SingleModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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640
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SingleReadQ</span><span class="p">,</span> <span class="n" style="color: #333;">SingleHit</span><span class="p">,</span> <span class="n" style="color: #333;">SingleQModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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641
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PairedEndRead</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndHit</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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642
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PairedEndReadQ</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndHit</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndQModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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643
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Unknown Read Type!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">N1</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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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: There are no alignable reads!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">theta</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">thetaF</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.theta"</span><span class="p">,</span> <span class="n" style="color: #333;">statName</span><span class="p">);</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">fo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">thetaF</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fo</span><span class="p">);</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">modelF</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.model"</span><span class="p">,</span> <span class="n" style="color: #333;">statName</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">fo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">modelF</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fo</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">eel</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</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;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">eel</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcripts</span><span class="p">.</span><span class="n" style="color: #333;">getTranscriptAt</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">getLength</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">countv</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">[</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">countv</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">writeResultsEM</span><span class="p">(</span><span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">refName</span><span class="p">,</span> <span class="n" style="color: #333;">imdName</span><span class="p">,</span> <span class="n" style="color: #333;">transcripts</span><span class="p">,</span> <span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">eel</span><span class="p">,</span> <span class="n" style="color: #333;">countv</span><span class="p">,</span> <span class="n" style="color: #333;">appendNames</span><span class="p">);</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">genBamF</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">outBamF</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.transcript.bam"</span><span class="p">,</span> <span class="n" style="color: #333;">outName</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">command</span><span class="p">[</span><span class="mi" style="color: #099;">1005</span><span class="p">];</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="s" style="color: #d14;">"cp %s %s"</span><span class="p">,</span> <span class="n" style="color: #333;">inpSamF</span><span class="p">,</span> <span class="n" style="color: #333;">outBamF</span><span class="p">);</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">command</span><span class="p">);</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">system</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">);</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">countv</span><span class="p">;</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">READ_INT_TYPE</span><span class="p">)</span><span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">N1</span><span class="p">)</span> <span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//set model parameters</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</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;">N0</span><span class="p">;</span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</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;">N1</span><span class="p">;</span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N2</span><span class="p">;</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">refs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.mparams"</span><span class="p">,</span> <span class="n" style="color: #333;">imdName</span><span class="p">);</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">);</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">general_assert</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Cannot open "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cstrtos</span><span class="p">(</span><span class="n" style="color: #333;">mparamsF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"It may not exist."</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">minL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">maxL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">probF</span><span class="p">;</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 0 or 1 , for estRSPD</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span><span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">estRSPD</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</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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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mate_minL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mate_maxL</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">sd</span><span class="p">;</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">mparams</span><span class="p">.</span><span class="n" style="color: #333;">seedLen</span><span class="p">;</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">fin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//run EM</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">read_type</span><span class="p">)</span> <span class="p">{</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SingleRead</span><span class="p">,</span> <span class="n" style="color: #333;">SingleHit</span><span class="p">,</span> <span class="n" style="color: #333;">SingleModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SingleReadQ</span><span class="p">,</span> <span class="n" style="color: #333;">SingleHit</span><span class="p">,</span> <span class="n" style="color: #333;">SingleQModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PairedEndRead</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndHit</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span> <span class="p">:</span> <span class="n" style="color: #333;">EM</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PairedEndReadQ</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndHit</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndQModel</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Unknown Read Type!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">time_t</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/rsem/commit/a87d5923b625c95c335e7664764c07e804107125#ef1025cc6f59414d24509fa38c7357a10e37a970"><strong>WriteResults.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +86,8 @@ void calcExpressionValues(int M, const std::vector<double>& theta, const std::ve</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">frac</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theta</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">frac</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"> <span class="p">}</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">general_assert</span><span class="p">(</span><span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">EPSILON</span><span class="p">,</span> <span class="s" style="color: #d14;">"No alignable reads?!"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// general_assert(denom >= EPSILON, "No alignable reads?!");</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">EPSILON</span><span class="p">)</span> <span class="n" style="color: #333;">denom</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>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</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;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">frac</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">denom</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//calculate FPKM</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -98,6 +99,7 @@ void calcExpressionValues(int M, const std::vector<double>& theta, const std::ve</td>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">tpm</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">M</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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</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;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fpkm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">EPSILON</span><span class="p">)</span> <span class="n" style="color: #333;">denom</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>
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101
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</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;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpkm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1e6</span><span class="p">;</span> </span>
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102
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"><span class="p">}</span></span>
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103
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -173,7 +175,7 @@ void writeResultsEM(int M, const char* refName, const char* imdName, Transcripts</td>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="n" style="color: #333;">j</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="LC176" class="line" lang="c"> <span class="n" style="color: #333;">isopct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">isopct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">EPSILON</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">tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">glens</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tlens</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">isopct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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178
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">gene_eels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">eel</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">isopct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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179
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="205" style="width: 35px; color: rgba(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">@@ -203,7 +205,7 @@ void writeResultsEM(int M, const char* refName, const char* imdName, Transcripts</td>
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203
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="p">}</span></span>
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204
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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205
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<td class="diff-line-num new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="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">
206
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<td class="diff-line-num new_line old" 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="LC206" class="line" lang="c"> <span class="n" style="color: #333;">ta_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t<span class="idiff left">pm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trans_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">ta_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t<span class="idiff left">rans_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">EPSILON</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">tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trans_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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207
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<td class="diff-line-num new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">trans_lens</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tlens</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ta_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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208
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="n" style="color: #333;">trans_eels</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">eel</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ta_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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209
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" style="width: 35px; color: rgba(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="216" style="width: 35px; color: rgba(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">@@ -214,7 +216,7 @@ void writeResultsEM(int M, const char* refName, const char* imdName, Transcripts</td>
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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
214
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> </span>
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215
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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">EPSILON</span><span class="p">)</span> <span class="p">{</span></span>
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216
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt</span><span class="p">.</span><span class="n" style="color: #333;">spAt</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">),</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gt</span><span class="p">.</span><span class="n" style="color: #333;">spAt</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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217
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<td class="diff-line-num new_line old" data-linenumber="219" style="width: 35px; color: rgba(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="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">gt_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">trans_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">gt_pct</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">EPSILON</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">trans_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gene_tpm</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/rsem/commit/a87d5923b625c95c335e7664764c07e804107125#5ae6fa11155cf92496c7c4bc847d0d0e467680bf"><strong>rsem-calculate-expression</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">@@ -417,25 +417,11 @@ if (!$is_alignment) {</td>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="perl"><span class="s" style="color: #d14;"> "</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">outFileNamePrefix</span> <span class="nv" style="color: #008080;">$imdName</span> <span class="s" style="color: #d14;">";</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="perl"><span class="s" style="color: #d14;"> ##</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="perl"><span class="s" style="color: #d14;">#<<<<<<< HEAD</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="perl"><span class="s" style="color: #d14;"> #if ( $gzipped_read_file ) {</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="perl"><span class="s" style="color: #d14;"> # $command .= ' --readFilesCommand zcat ';</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="perl"><span class="s" style="color: #d14;"> #} elsif ( $bzipped_read_file ) {</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="perl"><span class="s" style="color: #d14;"> # $command .= ' --readFilesCommand bzcat ';</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="perl"><span class="s" style="color: #d14;"> #}</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="perl"><span class="s" style="color: #d14;"> #if ( $read_type == 0 || $read_type == 1 ) {</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="perl"><span class="s" style="color: #d14;"> # $command .= "</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">readFilesIn</span> <span class="nv" style="color: #008080;">$mate1_list</span> <span class="s" style="color: #d14;">";</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="perl"><span class="s" style="color: #d14;"> #} else {</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="perl"><span class="s" style="color: #d14;"> # $command .= "</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">readFilesIn</span> <span class="nv" style="color: #008080;">$mate1_list</span> <span class="nv" style="color: #008080;">$mate2_list</span><span class="s" style="color: #d14;">";</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="perl"><span class="s" style="color: #d14;"> #}</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="perl"><span class="s" style="color: #d14;">#=======</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="perl"><span class="s" style="color: #d14;"> if ( $star_gzipped_read_file ) {</span></span>
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="perl"><span class="s" style="color: #d14;"> $command .= ' --readFilesCommand zcat ';</span></span>
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435
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="perl"><span class="s" style="color: #d14;"> } elsif ( $star_bzipped_read_file ) {</span></span>
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436
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="perl"><span class="s" style="color: #d14;"> $command .= ' --readFilesCommand bzip2 -c ';</span></span>
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437
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="perl"><span class="s" style="color: #d14;"> }</span></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="perl"><span class="s" style="color: #d14;">#>>>>>>> master</span></span>
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439
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>
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440
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="perl"><span class="s" style="color: #d14;"> if ( $read_type == 0 || $read_type == 1 ) {</span></span>
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441
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="perl"><span class="s" style="color: #d14;"> $command .= "</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">readFilesIn</span> <span class="nv" style="color: #008080;">$mate1_list</span> <span class="s" style="color: #d14;">";</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="552" style="width: 35px; color: rgba(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="538" style="width: 35px; color: rgba(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">@@ -552,13 +538,24 @@ if ($quiet) { $command .= " -q"; }</td>
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552
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="perl"></span>
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553
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="perl"><span class="s" style="color: #d14;">&runCommand($command);</span></span>
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554
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="perl"></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="perl"><span class="s" style="color: #d14;">$command = "rsem-build-read-index $gap"; </span></span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="perl"><span class="s" style="color: #d14;">if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; }</span></span>
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557
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="perl"><span class="s" style="color: #d14;">elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; }</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="perl"><span class="s" style="color: #d14;">elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="perl"><span class="s" style="color: #d14;">elsif ($read_type == 3) { $command .= " 1 $quiet $imdName\_alignable_1.fq $imdName\_alignable_2.fq"; }</span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="perl"><span class="s" style="color: #d14;">else { print "Impossible! read_type is not in [1,2,3,4]!\n"; exit(-1); }</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="perl"><span class="s" style="color: #d14;">&runCommand($command);</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="perl"><span class="s" style="color: #d14;">my $inpCntF = "$statName.cnt";</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="perl"><span class="s" style="color: #d14;">my $local_status = open(INPUT, $inpCntF);</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="perl"><span class="s" style="color: #d14;">if ($local_status == 0) { print "Fail to open file $inpF!\n"; exit(-1); }</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="perl"><span class="s" style="color: #d14;">my $line = <INPUT>;</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="perl"><span class="s" style="color: #d14;">chomp($line);</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="perl"><span class="s" style="color: #d14;">my @Ns = split(/ /, $line);</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="perl"><span class="s" style="color: #d14;">close(INPUT);</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="perl"><span class="s" style="color: #d14;">my $no_aligned = ($Ns[1] == 0);</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="perl"></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="perl"><span class="s" style="color: #d14;">if (!$no_aligned) {</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="perl"><span class="s" style="color: #d14;"> $command = "rsem-build-read-index $gap"; </span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="perl"><span class="s" style="color: #d14;"> if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; }</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="perl"><span class="s" style="color: #d14;"> elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; }</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="perl"><span class="s" style="color: #d14;"> elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; }</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="perl"><span class="s" style="color: #d14;"> elsif ($read_type == 3) { $command .= " 1 $quiet $imdName\_alignable_1.fq $imdName\_alignable_2.fq"; }</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="perl"><span class="s" style="color: #d14;"> else { print "Impossible! read_type is not in [1,2,3,4]!\n"; exit(-1); }</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="perl"><span class="s" style="color: #d14;"> &runCommand($command); </span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl"><span class="s" style="color: #d14;">}</span></span>
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562
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="perl"></span>
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563
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="perl"><span class="s" style="color: #d14;">my $doesOpen = open(OUTPUT, ">$imdName.mparams");</span></span>
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564
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="perl"><span class="s" style="color: #d14;">if ($doesOpen == 0) { print "Cannot generate $imdName.mparams!\n"; exit(-1); }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -628,6 +625,20 @@ if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }</td>
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628
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="perl"></span>
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629
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="perl"><span class="s" style="color: #d14;">if ($mTime) { $time_start = time(); }</span></span>
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630
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="perl"></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="perl"><span class="s" style="color: #d14;">if ($no_aligned) { </span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="perl"><span class="s" style="color: #d14;"> print "Since no aligned reads, further steps will not be performed!\n";</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="perl"><span class="s" style="color: #d14;"> if (!$keep_intermediate_files) {</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="perl"><span class="s" style="color: #d14;"> &runCommand("rm -rf $temp_dir", "Fail to delete the temporary folder!");</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="perl"><span class="s" style="color: #d14;"> }</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="perl"><span class="s" style="color: #d14;"> if ($mTime) { </span></span>
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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="perl"><span class="s" style="color: #d14;"> open(OUTPUT, ">$sampleName.time");</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="perl"><span class="s" style="color: #d14;"> print OUTPUT "Aligning reads: $time_alignment s.\n";</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="perl"><span class="s" style="color: #d14;"> print OUTPUT "Estimating expression levels: $time_rsem s.\n";</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="perl"><span class="s" style="color: #d14;"> close(OUTPUT);</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="perl"><span class="s" style="color: #d14;"> }</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="perl"><span class="s" style="color: #d14;"> exit(0); </span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="perl"><span class="s" style="color: #d14;">}</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="perl"></span>
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631
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642
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="perl"><span class="s" style="color: #d14;">if ($calcPME || $calcCI ) {</span></span>
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632
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="perl"><span class="s" style="color: #d14;"> $command = "rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP";</span></span>
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633
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="perl"><span class="s" style="color: #d14;"> $command .= " -p $nThreads";</span></span>
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