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<h3>
Andreas Tille pushed to branch master
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/aaab3023e8cc317dfe81d6ee977f0ab498b59572">aaab3023</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-12T09:30:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rsem/commit/ae87a66055d688c9370604504161747f7eb5c0d0">ae87a660</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-12T09:31:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">s/python/python3/ in (Build-)Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rsem/commit/161ec43a904b7044e20cac2c862addc2a521b460">161ec43a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-12T09:39:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rsem/commit/9fd728aab68e7301baa525a77ff5b0c0f51f2ff0">9fd728aa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-12T09:45:40Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rsem/compare/f664f39bf739f053594f9707edac918019420c0b...9fd728aab68e7301baa525a77ff5b0c0f51f2ff0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rsem (1.3.2+dfsg-2) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #938415</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 12 Sep 2019 11:39:48 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">rsem (1.3.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/rsem/compare/f664f39bf739f053594f9707edac918019420c0b...9fd728aab68e7301baa525a77ff5b0c0f51f2ff0#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rsem/compare/f664f39bf739f053594f9707edac918019420c0b...9fd728aab68e7301baa525a77ff5b0c0f51f2ff0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,12 +4,12 @@ Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libncurses5-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libboost-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> perl,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> help2man,</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># bowtie is a run-time dependency available on only a few systems, not actually</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> r-base-core,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> bowtie | bowtie2,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> python</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python<span class="idiff left right">3</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Suggests: r-bioc-ebseq</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: RNA-Seq by Expectation-Maximization</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> RSEM is a software package for estimating gene and isoform expression</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/rsem/compare/f664f39bf739f053594f9707edac918019420c0b...9fd728aab68e7301baa525a77ff5b0c0f51f2ff0#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/938415</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Thu, 12 Sep 2019 11:26:11 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/pRSEM/Gene.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/Gene.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -124,7 +124,7 @@</span> def constructGenesFromTranscripts(transc</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> genes = []</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> gene_dict_id = {}</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> for tr in transcripts:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if gene_dict_id.has_key(tr.gene_id):</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if tr.gene_id in gene_dict_id:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> gene_dict_id[tr.gene_id].transcripts.append(tr)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> tr.gene = gene_dict_id[tr.gene_id]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span> def constructGenesFromTranscripts(transc</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> gene_dict_id[tr.gene_id] = gene</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> tr.gene = gene</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list(map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes));</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> return genes;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/Param.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/Param.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -98,7 +98,7 @@</span> class Param:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> def __str__(self):</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ss = [ "%-33s %s\n" % (key, val) for (key, val) in self.argdict.items()] + \</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ss = [ "%-33s %s\n" % (key, val) for (key, val) in list(self.argdict.items())] + \</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> [ "%-33s %s\n" % ('RSEM_temp_dir', self.temp_dir ) ] + \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> [ "%-33s %s\n" % ('pRSEM_scr_dir', self.prsem_scr_dir) ]</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> return ''.join(ss)</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -109,7 +109,7 @@</span> class Param:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> prm = cls()</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> prm.argdict = argdict</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (key, val) in argdict.items():</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (key, val) in list(argdict.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> setattr(prm, key, val)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> if prm.imd_name is not None:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/Prsem.py</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/Prsem.py</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> __doc__="""</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -65,9 +65,9 @@</span> def buildTrainingSet(prm):</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> The order is required by rsem-run-gibbs so that prior can be assigned to</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> transcript correctly</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ogot_genes = filter(lambda g: len(g.transcripts) == 1 and</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ogot_genes = [g for g in prm.genes if len(g.transcripts) == 1 and</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> (g.end - g.start + 1) >=</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prm.TRAINING_GENE_MIN_LEN, prm.genes)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prm.TRAINING_GENE_MIN_LEN]</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> trs = [tr for g in ogot_genes for tr in g.transcripts]</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -127,7 +127,7 @@</span> def genPriorByCombinedTSSSignals(prm):</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> f_fout = open(prm.finfo_multi_targets, 'w')</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> f_fout.write("targetid\tfaln\tfftrs\n")</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (tgtid, faln) in prm.targetid2fchipseq_alignment.items():</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (tgtid, faln) in list(prm.targetid2fchipseq_alignment.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> fftrs = prm.imd_name + '_prsem.' + tgtid + '.all_tr_features'</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> f_fout.write("%s\t%s\t%s\n" % (tgtid, faln, fftrs))</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> f_fout.close()</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/Transcript.py</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/Transcript.py</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -41,7 +41,7 @@</span> class Transcript:</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> for (start, end) in self.exon_ranges:</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> s += " %d %d" % (start, end);</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> s += "\n";</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key in self.gtf_attr.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key in list(self.gtf_attr.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> for val in self.gtf_attr[key]:</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> s += '%s "%s"; ' % (key, val);</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> s = s.rstrip();</span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> class Transcript:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> for feature_word in feature_words:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> feature_word.lstrip();</span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> (key, val) = feature_word.split();</span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not self.gtf_attr.has_key(key):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if key not in self.gtf_attr:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> self.gtf_attr[key] = [];</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> self.gtf_attr[key].append(val.strip('"'));</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -160,7 +160,7 @@</span> def readRSEMTI(fin):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> tr.constructFromRSEMTI(lines[i*6+1:i*6+7]);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> transcripts.append(tr);</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> if (i > 0) and (i % 20000 == 0):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "processed %d transcripts" % i;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("processed %d transcripts" % i);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> return transcripts;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -183,7 +183,7 @@</span> def quicklyReadRSEMTI(fin):</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> tr.quicklyConstructFromRSEMTI(lines[i*6+1:i*6+7]);</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> transcripts.append(tr);</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> if (i > 0) and (i % 20000 == 0):</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "processed %d transcripts" % i;</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("processed %d transcripts" % i);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
</pre>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> return transcripts;</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/Util.py</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/Util.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> def runCommandAndGetOutput(*args, **kwar</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> try:</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> output = subprocess.check_output(str_args)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except subprocess.CalledProcessError, e:</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except subprocess.CalledProcessError as e:</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> sys.exit("\nExecution failed: %s\n" % e.output)</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> return output</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="p">@@ -123,14 +123,14 @@</span> def runMPOverAList(nprocs, func, args):</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> if len(args[0]) > nprocs:</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> chunksize = len(args[0])/nprocs + 1</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> procs = []</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(nprocs):</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(nprocs):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> list_args = [args[0][chunksize*i:chunksize*(i+1)]] + args[1:] + [out_q]</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> p = mp.Process(target = func, args = tuple(list_args))</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> procs.append(p)</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> p.start()</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> dict_to_return = {}</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(nprocs):</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(nprocs):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> dict_to_return.update(out_q.get())</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> for p in procs:</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/prsem-calculate-expression</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/prsem-calculate-expression</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> __doc__="""</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/prsem-prepare-reference</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/prsem-prepare-reference</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> __doc__="""</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pRSEM/prsem-testing-procedure</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pRSEM/prsem-testing-procedure</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> </span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> __doc__="""</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rsem-gff3-to-gtf</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rsem-gff3-to-gtf</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> # Copyright (c) 2016</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> # Bo Li (University of California, Berkeley)</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/rsem-refseq-extract-primary-assembly</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/rsem-refseq-extract-primary-assembly</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> from sys import argv, exit</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/rsem/compare/f664f39bf739f053594f9707edac918019420c0b...9fd728aab68e7301baa525a77ff5b0c0f51f2ff0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_debian_packaged_samtools.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">2to3.patch</span></pre>
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